LMU BioDB 2024 - User contributions [en]

Ckaplan Week 15

2024-05-03T02:22:04Z

Ckapla12: adding my reflection

[[File:Yeast_Beasts_Presentation.pdf]]

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

The week 14 and 15 reflections will be combined, as advised by Dr. Dahlquist. This is because of the wiki being intermittently down during week 14.

See our data analyst week 14 progress here: [[Data Analysts Week 14]]

See our data analyst week 15 progress here: [[Data Analysts Week 15]]

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. For Milestone 5, we followed the procedure listed on [[Data Analysis]]. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing these milestones, and her help was very valuable. [[User:Msymond1| Dean Symonds]] assisted us in creating an input workbook for GRNmap using queries to the Microsoft Access database created by the Coders/Designers.

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 15. Retrieved May 2, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

{{Yeast Beasts}}
[[Category:Journal Entry]]
[[Category:Team Project]]

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:12, 2 May 2024 (PDT)

{{ckaplan}}

Yeast Beasts

2024-05-03T02:21:20Z

Ckapla12: finishing reflection

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 14===
===Week 15===
====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

Ckaplan Week 15

2024-05-03T02:12:12Z

Ckapla12: signature

Data Analysts Week 15

2024-05-03T02:10:44Z

Ckapla12: fixing acknowledgements and references, adding signature

===Milestone 5===
#We created a gene regulatory network for GRNmap using using the Access database that the Coders/Designers made.
#[[User:Msymond1| Dean Symonds]] assisted us in creating an input workbook for GRNmap using queries to the Microsoft Access database created by the Coders/Designers.

The queries were created as follows:
*production_rates
*degradation_rates
*wt_log2_expression (based on the CHP-treated data)
*network

*We sent our data to Dr. Dahlquist and she helped us interpret the data.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. For Milestone 5, we followed the procedure listed on [[Data Analysis]]. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing these milestones, and her help was very valuable. [[User:Msymond1| Dean Symonds]] assisted us in creating an input workbook for GRNmap using queries to the Microsoft Access database created by the Coders/Designers.

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 15. Retrieved May 2, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

{{Yeast Beasts}}
[[Category:Journal Entry]]
[[Category:Team Project]]

Except for what is noted above, this entry was completed by Katie and Charlotte and not copied from another source. [[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:10, 2 May 2024 (PDT)

Ckaplan Week 15

2024-05-03T02:08:43Z

Ckapla12: editing link

Ckaplan Week 15

2024-05-03T02:08:12Z

Ckapla12: editing references and acknowledgements

Data Analysts Week 15

2024-05-03T01:55:04Z

Ckapla12: format

===Milestone 5===
#We created a gene regulatory network for GRNmap using using the Access database that the Coders/Designers made.
#[[User:Msymond1| Dean Symonds]] assisted us in creating an input workbook for GRNmap using queries to the Microsoft Access database created by the Coders/Designers.

The queries were created as follows:
*production_rates
*degradation_rates
*wt_log2_expression (based on the CHP-treated data)
*network

*We sent our data to Dr. Dahlquist and she helped us interpret the data.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 18:54, 2 May 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 15. Retrieved May 2, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

{{Yeast Beasts}}
[[Category:Journal Entry]]
[[Category:Team Project]]

Data Analysts Week 15

2024-05-03T01:54:54Z

Ckapla12: references and acknowledgement

===Milestone 5===
#We created a gene regulatory network for GRNmap using using the Access database that the Coders/Designers made.
#[[User:Msymond1| Dean Symonds]] assisted us in creating an input workbook for GRNmap using queries to the Microsoft Access database created by the Coders/Designers.

The queries were created as follows:
*production_rates
*degradation_rates
*wt_log2_expression (based on the CHP-treated data)
*network

*We sent our data to Dr. Dahlquist and she helped us interpret the data.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 18:54, 2 May 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 15. Retrieved May 2, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

{{Yeast Beasts}}
[[Category:Journal Entry]]
[[Category:Team Project]]

Data Analysts Week 15

2024-05-03T01:53:17Z

Ckapla12: finishing milestone 5

Data Analysts Week 15

2024-05-03T01:27:51Z

Ckapla12: format

===Milestone 5===

Data Analysts Week 15

2024-05-03T01:27:34Z

Ckapla12: creating milestone 5

===Milestone 5:===

Ckaplan Week 15

2024-05-03T01:18:12Z

Ckapla12: linking our data analyst week 15 page

Ckaplan Week 15

2024-05-03T01:16:28Z

Ckapla12: linking to our data analysts week 14 page, adding acknowledgments and references and yeast beasts template

Ckaplan Week 15

2024-05-03T01:14:51Z

Ckapla12: explaining combined reflection

User:Ckapla12

2024-05-03T01:13:20Z

Ckapla12: adding data analysts week 15

==Charlotte Kaplan==

===Contact information===

* School email: ckapla12@lion.lmu.edu
Mailbox Address:
Loyola Marymount University
1 LMU Drive, MS-6275
Los Angeles, CA 90045-2659

[[File:mypictureckaplan123.jpeg]]

===Education===

[https://cse.lmu.edu/department/biology/ Lmu Biology Department]

* Major: Biology
* Minors: Women's' Studies and Environmental Science
* Graduation: 2026
* Upper division courses:
# Cell Biology Lab
# Biological Databases
# Genetics

=====Career Interests:=====

*Biotechnology- exploring vaccines and pharmaceuticals
**Dream is to develop medication and supplements for women's' health
***I have not yet been involved in research, but I am incredibly interested!

===Work experience===
Supervisor
*Presto Pasta
*May 2020 through May 2021
*Managed employees, served, packaged to go orders, kept track of income and stock
Body Contouring Specialist
*California Body Contouring
*December 2021 through August 2023
*Gave consultations, provided contouring services to customers

===Personal Interests===
*Animals
*Cooking
*Baking
*Shopping
*Family and Friends
*Beauty

[[image:mycatbiggles.jpg|200px|Image: 200 pixels]]

Here is my cat Mr. Biggles, I love animals so much!

-Favorite aspect of Biology:

I absolutely love studying biology, especially when it comes to cells and genetics. I dream of being part of research that uncovers new things at this level. Understanding how our bodies and brains work is also something I find fascinating. On top of that, I'm really into animals and figuring out how they live in their environments. The idea of contributing to scientific discoveries in these areas makes me super excited about the wonders of biology.

-Favorite aspect of Computer Science:
I do not know much about computer science, but I am excited to learn simple coding skills.

== References ==
Hailey Ivanson: my homework partner. We communicated over text and checked each other's wiki pages on January 17th 2024. https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/User:Hivanson

LMU BioDB 2024. (2024). Week 1. Retrieved January 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_1

Help: Images. (2023). Simple English Wikipedia, the Free Encyclopedia. Retrieved January 17, 2023, from https://simple.wikipedia.org/w/index.php?title=Help:Images&oldid=8989438

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 20:03, 17 January 2024 (PST)

===Acknowledgements===

Hailey Ivanson: my homework partner. We communicated over text and checked each other's wiki pages on January 17th 2024. https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/User:Hivanson

-sent to me by my homework partner, Hailey Ivanson, to help me resize my images.



{{Ckaplan}}

[[Data Analysts Week 13]]

[[Data Analysts Week 14]]

[[Data Analysts Week 15]]

User:Ckapla12

2024-05-03T01:12:52Z

Ckapla12: deleting my week 14/15

Ckaplan Week 14/15

2024-05-03T01:10:49Z

Ckapla12: creating page

week 14 and 15 were combined due to the wiki being down.

User:Ckapla12

2024-05-03T01:10:24Z

Ckapla12:

Ckaplan Week 13

2024-05-03T01:07:48Z

Ckapla12: acknowledgements and references

Data Analysts: Katie and Charlotte

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

see our work for week 13 here: [[Data Analysts Week 13]]

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 18:06, 2 May 2024 (PDT)

{{Yeast Beasts}}
[[Category:Journal Entry]]
[[Category:Team Project]]

Ckaplan Week 13

2024-05-03T01:06:28Z

Ckapla12: adding signature

Ckaplan Week 13

2024-05-03T01:05:06Z

Ckapla12: linking to data analysts week 13

Ckaplan Week 13

2024-05-03T01:04:20Z

Ckapla12: uploading my reflection from week 13.

Ckaplan Week 15

2024-05-03T01:00:40Z

Ckapla12: invoking template

[[File:Yeast_Beasts_Presentation.pdf]]

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

{{ckaplan}}

Ckaplan Week 15

2024-05-03T01:00:15Z

Ckapla12: reuploading presentation

[[File:Yeast_Beasts_Presentation.pdf]]

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

Yeast Beasts

2024-05-02T06:28:19Z

Ckapla12: presentation upload

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 14===
===Week 15===
# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

[[File:Yeast_Beasts_Presentation.pdf]]

{{Yeast_Beasts}}
[[Template:Yeast_Beasts]]

Ckaplan Week 15

2024-05-02T06:27:08Z

Ckapla12: our presentation

[[File:Yeast_Beasts_Presentation.pdf]]

Ckaplan Week 15

2024-05-02T06:20:26Z

Ckapla12: uploading presentation

[[Media: Yeast_Beasts_Presentation.zip]]

Ckaplan Week 15

2024-05-02T06:19:39Z

Ckapla12: Created page with "Media: Yeast Beasts Presentation.zip"

[[Media: Yeast Beasts Presentation.zip]]

User:Ckapla12

2024-05-02T06:19:19Z

Ckapla12: week 15

Data Analysts Week 14

2024-04-25T21:48:52Z

Ckapla12: editing procedure

===Continuing Milestone 3===
[[User:Hivanson| Hailey Ivanson]] helped Katie and I with the Bonferroni and B-H values.
#We used the formula =IFCHP_Bonferroni_p-value>1,1,CHP_Bonferroni_p-value) and =IFControl_Bonferroni_p-value>1,1,Control_Bonferroni_p-value)
#we inserted a new worksheet named "CHP_ANOVA_B-H" and "Control_ANOVA_B-H."
#we copied and pasted the "MasterIndex", "ID", and "Standard Name" columns from our previous worksheet into the first two columns of the new worksheet.
#We used Paste special > Paste values and copied our unadjusted p values from our ANOVA worksheet and pasted it into Column D.
#We selected all of columns A, B, C, and D and sorted by ascending values, smallest to largest.
#We typed "Rank" in cell E1. we typed "1" into cell E2 and "2" into cell E3. Then we selected both cells E2 and E3 and double clicked on the plus sign to fill the column with a series of numbers from 1 to 4697.
#[[User:Hivanson| Hailey Ivanson]] assisted us in calculating the Benjamini and Hochberg p value correction. We typed CHP_B-H_p-value and repeated for the control. We copied that equation to the entire column. =(D2*4697)/E2
#We then typed "CHP_B-H_p-value" into cell G1.
#In cell G2: we used the equation =IF(F2>1,1,F2) and copied that equation to the entire column.
#We selected columns A through G and sorted them in ascending order.
#We copied column G and used Paste special > Paste values to paste it into the next column of our ANOVA sheet.
#We zipped and uploaded the .xlsx file.
#We performed a sanity check by selecting row 1: Data > Filter > Autofilter- p value less than 0.05

Sanity Check Results:
*CONTROL
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
3699
<.01
3219
<.001
2558
<.0001
1921
<.00001
1325;

*CHP
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
2863
<.01
2403
<.001
1884
<.0001
1435; 30.55%
<.00001
1076; 22.91%

===Milestone 4===
#We inserted a new worksheet and named it "CHP_stem".
#We selected all of the data from the "CHP_ANOVA" worksheet and Paste special > paste values into the "CHP_stem" worksheet.
#"Master_Index" was renamed to "SPOT". Column B named "ID" was renamed to "Gene Symbol". We deleted the column named "Standard_Name".
#We filtered the data on the B-H corrected p value to be > 0.05.
#We selected all of the rows except for the header row and deleted the rows by right-clicking and choosing "Delete Row" from the context menu. Then we undid this filter.
#We deleted all of the data columns except for the Average Log Fold change columns for each timepoint.
#we renamed the data columns with just the time and units.
#We clicked "Replace all" to remove the #DIV/0! errors.
#We saved this spreadsheet as Text (Tab-delimited) (*.txt).
#We downloaded the stem.zip file and selected "Extract all" from the menu, creating a folder called stem.
#We clicked on the "Profile GO Table" to see the list of Gene Ontology. We saved the file to our desktop.
#We clicked on the "Profile Gene Table" button to see the list of genes belonging to the profile.

4/24/24
Milestone 4
P value >0.00001
41 and 7 significant profiles

Profile 41 grnsight:
Rpn4
Gcn4
Pdr1
Xbp1
Met28
Mga2
Spt23
Bas1
Yap1
Sok2
Msn2
Crz1
Rlm1
Fhl1
Pdr3
Cbf1
Rph1
Met31
Stp1
Msn4
Tec1
Rgm1
Stp2

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:28, 23 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

Data Analysts Week 14

2024-04-25T21:38:51Z

Ckapla12: adding information

===Continuing Milestone 3===
[[User:Hivanson| Hailey Ivanson]] helped Katie and I with the Bonferroni and B-H values.
#We used the formula =IFCHP_Bonferroni_p-value>1,1,CHP_Bonferroni_p-value) and =IFControl_Bonferroni_p-value>1,1,Control_Bonferroni_p-value)
#we inserted a new worksheet named "CHP_ANOVA_B-H" and "Control_ANOVA_B-H."
#we copied and pasted the "MasterIndex", "ID", and "Standard Name" columns from our previous worksheet into the first two columns of the new worksheet.
#We used Paste special > Paste values and copied our unadjusted p values from our ANOVA worksheet and pasted it into Column D.
#We selected all of columns A, B, C, and D and sorted by ascending values, smallest to largest.
#We typed "Rank" in cell E1. we typed "1" into cell E2 and "2" into cell E3. Then we selected both cells E2 and E3 and double clicked on the plus sign to fill the column with a series of numbers from 1 to 4697.
#[[User:Hivanson| Hailey Ivanson]] assisted us in calculating the Benjamini and Hochberg p value correction. We typed CHP_B-H_p-value and repeated for the control. We copied that equation to the entire column. =(D2*4697)/E2
#We then typed "CHP_B-H_p-value" into cell G1.
#In cell G2: we used the equation =IF(F2>1,1,F2) and copied that equation to the entire column.
#We selected columns A through G and sorted them in ascending order.
#We copied column G and used Paste special > Paste values to paste it into the next column of our ANOVA sheet.
#We zipped and uploaded the .xlsx file.
#We performed a sanity check by selecting row 1: Data > Filter > Autofilter- p value less than 0.05

Sanity Check Results:
*CONTROL
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
3699
<.01
3219
<.001
2558
<.0001
1921
<.00001
1325;

*CHP
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
2863
<.01
2403
<.001
1884
<.0001
1435; 30.55%
<.00001
1076; 22.91%

===Milestone 4===
#We inserted a new worksheet and named it "CHP_stem".
#We selected all of the data from the "CHP_ANOVA" worksheet and Paste special > paste values into the "CHP_stem" worksheet.
#"Master_Index" was renamed to "SPOT". Column B named "ID" was renamed to "Gene Symbol". We deleted the column named "Standard_Name".
#We filtered the data on the B-H corrected p value to be > 0.05.
#We selected all of the rows except for the header row and deleted the rows by right-clicking and choosing "Delete Row" from the context menu. Then we undid this filter.
#We deleted all of the data columns except for the Average Log Fold change columns for each timepoint.
#we renamed the data columns with just the time and units.
#We clicked "Replace all" to remove the #DIV/0! errors.
#We saved this spreadsheet as Text (Tab-delimited) (*.txt).
#We downloaded the stem.zip file and selected "Extract all" from the menu, creating a folder called stem.

4/24/24
Milestone 4
P value >0.00001
41 and 7 significant profiles

Profile 41 grnsight:
Rpn4
Gcn4
Pdr1
Xbp1
Met28
Mga2
Spt23
Bas1
Yap1
Sok2
Msn2
Crz1
Rlm1
Fhl1
Pdr3
Cbf1
Rph1
Met31
Stp1
Msn4
Tec1
Rgm1
Stp2

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:28, 23 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

Data Analysts Week 14

2024-04-25T20:57:04Z

Ckapla12: milestone 4

===Continuing Milestone 3===
[[User:Hivanson| Hailey Ivanson]] helped Katie and I with the Bonferroni and B-H values.
#We used the formula =IFCHP_Bonferroni_p-value>1,1,CHP_Bonferroni_p-value) and =IFControl_Bonferroni_p-value>1,1,Control_Bonferroni_p-value)
#we inserted a new worksheet named "CHP_ANOVA_B-H" and "Control_ANOVA_B-H."
#we copied and pasted the "MasterIndex", "ID", and "Standard Name" columns from our previous worksheet into the first two columns of the new worksheet.
#We used Paste special > Paste values and copied our unadjusted p values from our ANOVA worksheet and pasted it into Column D.
#We selected all of columns A, B, C, and D and sorted by ascending values, smallest to largest.
#We typed "Rank" in cell E1. we typed "1" into cell E2 and "2" into cell E3. Then we selected both cells E2 and E3 and double clicked on the plus sign to fill the column with a series of numbers from 1 to 4697.
#[[User:Hivanson| Hailey Ivanson]] assisted us in calculating the Benjamini and Hochberg p value correction. We typed CHP_B-H_p-value and repeated for the control. We copied that equation to the entire column. =(D2*4697)/E2
#We then typed "CHP_B-H_p-value" into cell G1.
#In cell G2: we used the equation =IF(F2>1,1,F2) and copied that equation to the entire column.
#We selected columns A through G and sorted them in ascending order.
#We copied column G and used Paste special > Paste values to paste it into the next column of our ANOVA sheet.
#We zipped and uploaded the .xlsx file.
#We performed a sanity check by selecting row 1: Data > Filter > Autofilter- p value less than 0.05

Sanity Check Results:
*CONTROL
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
3699
<.01
3219
<.001
2558
<.0001
1921
<.00001
1325;

*CHP
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
2863
<.01
2403
<.001
1884
<.0001
1435; 30.55%
<.00001
1076; 22.91%

===Milestone 4===
#We inserted a new worksheet and named it "CHP_stem".
#We selected all of the data from the "CHP_ANOVA" worksheet and Paste special > paste values into the "CHP_stem" worksheet.
#"Master_Index" was renamed to "SPOT". Column B named "ID" was renamed to "Gene Symbol". We deleted the column named "Standard_Name".
#We filtered the data on the B-H corrected p value to be > 0.05.
#We selected all of the rows except for the header row and deleted the rows by right-clicking and choosing "Delete Row" from the context menu. Then we undid this filter.
#We deleted all of the data columns except for the Average Log Fold change columns for each timepoint.
#we renamed the data columns with just the time and units.
#We clicked "Replace all" to remove the #DIV/0! errors.
#We saved this spreadsheet as Text (Tab-delimited) (*.txt).
#We downloaded the stem.zip file and selected "Extract all" from the menu, creating a folder called stem.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:28, 23 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

Data Analysts Week 13

2024-04-23T21:45:41Z

Ckapla12: editing references

==Charlotte and Katie's Data Analyst Journal==

===Milestone 1===
Completed as of April 11th when we gave our Journal Club Presentation with [[User:Hivanson| Hailey Ivanson]]

===Milestone 2===
#With Quality Assurance team member [[User:Hivanson| Hailey Ivanson]], we downloaded and examined the microarray dataset: [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD Processed Data].
#We made a sample-data relationship table in Excel labeled "reorganized" that lists all of the samples and at which time point they were collected, and their replicate number. We came up with consistent column headers that summarize this information. We named each column either Control_LogFC_timepoint-replicatenumber or CHP_LogFC_timepoint-replicatenumber, as in Control_LogFC_0-1 and CHP_LogFC_0-1. The timepoint for each is either 0, 3 , 6, 12, 20, 40, 70, or 120, and the replicate number either 1, 2, or 3. We organized the data in a worksheet in an Excel workbook so that:
#*ID is the first column header, and within it are all of the SGD systemic names
#*Data columns are to the right, in increasing chronological order, using the column header pattern we created
#*Treatments are grouped together
#*Replicates are grouped together
#*We deleted the "EWEIGHT" row and "GWEIGHT" column.
#*We then had to undo the log-transformed raw intensity values. We first created new columns for each respective trial in the formats Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber, as in Control_FC_0-1 and CHP_FC_0-1. We then transformed the data in the first cell of each column with the equation <code>=2^<cell designation></code>, where the cell designation is the first cell of the respective Control_LogFC_timepoint-replicatenumber and CHP_LogFC_timepoint-replicatenumber columns, and then applied this command to the remaining cells of the column.
#*We then created a new worksheet labeled "with_averages", in which we copy and special pasted the values of the columns with headers Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber.
#*We then created new columns called Control_FC_0-avg and CHP_FC_0-avg to the right of their respective t0 timepoint trials, and then within them computed the average value of the t0 timepoint trials for the control and CHP-treated data. In the first cell below the column headed Control_FC_0-avg, we used the Excel command <code>=AVG(B2:D2)</code> and then applied this command to all cells in the column. In the first cell below the column headed CHP_FC_0-avg column, we used the command <code>=AVG(F2:H2)</code> and then applied this command to all cells in the column.
#*We then created new columns to the right of each treatment with a column header either Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Fold_Change_3-1 or CHP_Fold_Change_3-1. We then calculated the fold change by dividing the first cell of each trial by the average t0 value for the respective treatment (control or CHP-treated), and then applying this throughout the column. To the right of each new column, we also created created columns with a column header either Control_Log2_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Log2_Fold_Change_3-1 or CHP_Log2_Fold_Change_3-1. In each Log2 column, We then log2 transformed the fold changes by using <code>=LOG(cell designation, 2)</code>, where the cell designation is the first cell of the respective Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber columns. We then applied this throughout all of the cells in each Log2 column.

===Milestone 3===
#We created a new worksheet, naming it "CHP_ANOVA".
#We copied all the Control_Log2_Fold_Change_timepoint-replicatenumber and CHP_Log2_Fold_Change_timepoint-replicatenumber columns and special pasted only the values into the new worksheet.
#To the right of each group of either the Control or CHP replicates at one timepoint, we created columns with headers in the form Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint, where timepoint is either 3, 6, 12, 20, 40, 70, or 120.
# In the cell below the Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint headers, we typed =AVG(replicate 1 cell designation:replicate 3 cell designation), where the cell designations are the first cells of the replicate 1 at one timepoint and the replicate 3 at that same time point. This computed the average of replicate values, and we then applied this throughout the remaining cells in the column.
# To the right, we then copy and special pasted the values of each Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint columns. To the right of these, we created columns with the the headers Control_ss_HO and CHP_ss_HO.
#In the first cell below Control_ss_HO, we typed <code>=SUMSQ(B2,C2,D2,J2,K2,L2,R2,S2,T2,Z2,AA2,AB2,AH2,AI2,AJ2,AP2,AQ2,AR2,AX2,AY2,AZ2)</code> and clicked enter, and below CHP_ss_HO, we typed <code>=SUMSQ(F2,G2,H2,N2,O2,P2,V2,W2,X2,AD2,AE2,AF2,AL2,AM2,AN2,AT2,AU2,AV2,BB2,BC2,BD2)</code> and clicked enter.
#In the first cell below this header, we typed =SUMSQ for each of the time points.
#After this, we highlighted all of the LogFC data in row 2- not the AvgLogFC, and we pressed the enter key.
#We created the column headers Control_Log_FC_Time and CHP_Log_FC_Time.
#We used the equation =SUMSQ(<range of cells for logFC_t0-2>)-COUNTA(<range of cells for logFC_t0-2>)*<AvgLogFC_t0-2>^2 and hit enter for each of the rows that were not the average.
#The amount of data points we have is: 21. Number of time points we have is: 7.
#We replaced <range of cells for logFC_0-2> with the data range associated with t15 and so on for each time point.
#We replaced <AvgCHPLogFC_0-2> and <AvgControlLogFC_0-2> with the cell number that we computed the AvgCHPLogFC and AvgControlLogFC for 0-2, and the "^2" squares that value. This was repeated for each of time points across our data set.
#We created the column headers CHP_SS_full and Control_SS_full.
#Below this, we used the formula: =sum(<range of cells containing "ss" for each timepoint>) and hit enter.
#In the next two columns to the right, we created the headers CHP_Fstat and Control_Fstat as well as CHP_p-value and Control_p-value.
#Since n=21 and t=7, in the first cell of each Fstat column, we used the formula =((21-7)/7)*(<CHP_ss_HO>-<CHP_SS_full>)/<CHP_SS_full>) and hit enter. This same process was repeated for the control.
#We replaced the phrase CHP_ss_HO with the cell designation and replaced the phrase <CHP_SS_full> with the cell designation. This was also repeated for the control.
#Below the CHP_p-value header, we used the formula =FDIST(<CHP_Fstat>,7,21-7) replacing the phrase <CHP_Fstat> with the cell designation. We used this same formula for the Control_p-value column.
#We performed a sanity check by filtering our data so that the p value has to be less than 0.05.
#Before continuing, we undid any filters before we calculated the Bonferroni and p value corrections.
#We created two columns to the right called CHP_Bonferroni_p-value and Control_Bonferroni_p-value.
#We used the equations =<CHP_p-value>*4697 and =<Control_p-value>*4697
#

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 22:50, 17 April 2024 (PDT)
[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 13:59, 18 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

Data Analysts Week 14

2024-04-23T21:44:50Z

Ckapla12: editing references

===Continuing Milestone 3===
[[User:Hivanson| Hailey Ivanson]] helped Katie and I with the Bonferroni and B-H values.
#We used the formula =IFCHP_Bonferroni_p-value>1,1,CHP_Bonferroni_p-value) and =IFControl_Bonferroni_p-value>1,1,Control_Bonferroni_p-value)
#we inserted a new worksheet named "CHP_ANOVA_B-H" and "Control_ANOVA_B-H."
#we copied and pasted the "MasterIndex", "ID", and "Standard Name" columns from our previous worksheet into the first two columns of the new worksheet.
#We used Paste special > Paste values and copied our unadjusted p values from our ANOVA worksheet and pasted it into Column D.
#We selected all of columns A, B, C, and D and sorted by ascending values, smallest to largest.
#We typed "Rank" in cell E1. we typed "1" into cell E2 and "2" into cell E3. Then we selected both cells E2 and E3 and double clicked on the plus sign to fill the column with a series of numbers from 1 to 4697.
#[[User:Hivanson| Hailey Ivanson]] assisted us in calculating the Benjamini and Hochberg p value correction. We typed CHP_B-H_p-value and repeated for the control. We copied that equation to the entire column. =(D2*4697)/E2
#We then typed "CHP_B-H_p-value" into cell G1.
#In cell G2: we used the equation =IF(F2>1,1,F2) and copied that equation to the entire column.
#We selected columns A through G and sorted them in ascending order.
#We copied column G and used Paste special > Paste values to paste it into the next column of our ANOVA sheet.
#We zipped and uploaded the .xlsx file.
#We performed a sanity check by selecting row 1: Data > Filter > Autofilter- p value less than 0.05

Sanity Check Results:
*CONTROL
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
3699
<.01
3219
<.001
2558
<.0001
1921
<.00001
1325;

*CHP
How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 4697)?
2863
<.01
2403
<.001
1884
<.0001
1435; 30.55%
<.00001
1076; 22.91%

===Milestone 4===

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 3 and 4 protocol, linked here: [[Data Analysis]] The procedure for Milestone 3 was also adapted from the steps outlined in the [[Week 9]] assignment page. The procedure for Milestone 4 was also adapted from the steps outlined in the [[Week 10]] assignment page. Our quality assurance, [[User:Hivanson| Hailey Ivanson]] was a key part in completing this milestone, and her help was very valuable.
Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:28, 23 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 14. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14

LMU BioDB 2024. (2024). Week 9. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9

LMU BioDB 2024. (2024). Week 10. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10

LMU BioDB 2024. (2024). Data Analysis. Retrieved April 23, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis

Data Analysts Week 14

2024-04-23T21:43:41Z

Ckapla12: references

Data Analysts Week 14

2024-04-23T21:42:47Z

Ckapla12: editing acknowledgements

User:Ckapla12

2024-04-23T21:41:01Z

Ckapla12: format

User:Ckapla12

2024-04-23T21:40:45Z

Ckapla12: data week 14 link

Data Analysts Week 14

2024-04-23T21:36:34Z

Ckapla12:

Data Analysts Week 14

2024-04-23T21:36:19Z

Ckapla12: sanity check

Data Analysts Week 14

2024-04-23T21:32:39Z

Ckapla12: punctuation

Data Analysts Week 14

2024-04-23T21:30:34Z

Ckapla12: references. acknowledging hailey

Data Analysts Week 14

2024-04-23T21:28:21Z

Ckapla12: acknowledgements

Data Analysts Week 14

2024-04-23T21:16:18Z

Ckapla12: editing procedure

Data Analysts Week 14

2024-04-23T21:13:43Z

Ckapla12: beginning procedure. referencing our quality assurance.

Data Analysts Week 13

2024-04-18T21:59:23Z

Ckapla12: continuing with equations

Data Analysts Week 13

2024-04-18T21:44:18Z

Ckapla12: explaining formulas

==Charlotte and Katie's Data Analyst Journal==

===Milestone 1===
Completed as of April 11th when we gave our Journal Club Presentation with [[User:Hivanson| Hailey Ivanson]]

===Milestone 2===
#With Quality Assurance team member [[User:Hivanson| Hailey Ivanson]], we downloaded and examined the microarray dataset: [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD Processed Data].
#We made a sample-data relationship table in Excel labeled "reorganized" that lists all of the samples and at which time point they were collected, and their replicate number. We came up with consistent column headers that summarize this information. We named each column either Control_LogFC_timepoint-replicatenumber or CHP_LogFC_timepoint-replicatenumber, as in Control_LogFC_0-1 and CHP_LogFC_0-1. The timepoint for each is either 0, 3 , 6, 12, 20, 40, 70, or 120, and the replicate number either 1, 2, or 3. We organized the data in a worksheet in an Excel workbook so that:
#*ID is the first column header, and within it are all of the SGD systemic names
#*Data columns are to the right, in increasing chronological order, using the column header pattern we created
#*Treatments are grouped together
#*Replicates are grouped together
#*We deleted the "EWEIGHT" row and "GWEIGHT" column.
#*We then had to undo the log-transformed raw intensity values. We first created new columns for each respective trial in the formats Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber, as in Control_FC_0-1 and CHP_FC_0-1. We then transformed the data in the first cell of each column with the equation <code>=2^<cell designation></code>, where the cell designation is the first cell of the respective Control_LogFC_timepoint-replicatenumber and CHP_LogFC_timepoint-replicatenumber columns, and then applied this command to the remaining cells of the column.
#*We then created a new worksheet labeled "with_averages", in which we copy and special pasted the values of the columns with headers Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber.
#*We then created new columns called Control_FC_0-avg and CHP_FC_0-avg to the right of their respective t0 timepoint trials, and then within them computed the average value of the t0 timepoint trials for the control and CHP-treated data. In the first cell below the column headed Control_FC_0-avg, we used the Excel command <code>=AVG(B2:D2)</code> and then applied this command to all cells in the column. In the first cell below the column headed CHP_FC_0-avg column, we used the command <code>=AVG(F2:H2)</code> and then applied this command to all cells in the column.
#*We then created new columns to the right of each treatment with a column header either Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Fold_Change_3-1 or CHP_Fold_Change_3-1. We then calculated the fold change by dividing the first cell of each trial by the average t0 value for the respective treatment (control or CHP-treated), and then applying this throughout the column. To the right of each new column, we also created created columns with a column header either Control_Log2_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Log2_Fold_Change_3-1 or CHP_Log2_Fold_Change_3-1. In each Log2 column, We then log2 transformed the fold changes by using <code>=LOG(cell designation, 2)</code>, where the cell designation is the first cell of the respective Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber columns. We then applied this throughout all of the cells in each Log2 column.

===Milestone 3===
#We created a new worksheet, naming it "CHP_ANOVA".
#We copied all the Control_Log2_Fold_Change_timepoint-replicatenumber and CHP_Log2_Fold_Change_timepoint-replicatenumber columns and special pasted only the values into the new worksheet.
#To the right of each group of either the Control or CHP replicates at one timepoint, we created columns with headers in the form Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint, where timepoint is either 3, 6, 12, 20, 40, 70, or 120.
# In the cell below the Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint headers, we typed =AVG(replicate 1 cell designation:replicate 3 cell designation), where the cell designations are the first cells of the replicate 1 at one timepoint and the replicate 3 at that same time point. This computed the average of replicate values, and we then applied this throughout the remaining cells in the column.
# To the right, we then copy and special pasted the values of each Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint columns. To the right of these, we created columns with the the headers Control_ss_HO and CHP_ss_HO.
#In the first cell below Control_ss_HO, we typed <code>=SUMSQ(B2,C2,D2,J2,K2,L2,R2,S2,T2,Z2,AA2,AB2,AH2,AI2,AJ2,AP2,AQ2,AR2,AX2,AY2,AZ2)</code> and clicked enter, and below CHP_ss_HO, we typed <code>=SUMSQ(F2,G2,H2,N2,O2,P2,V2,W2,X2,AD2,AE2,AF2,AL2,AM2,AN2,AT2,AU2,AV2,BB2,BC2,BD2)</code> and clicked enter.
#In the first cell below this header, we typed =SUMSQ for each of the time points.
#After this, we highlighted all of the LogFC data in row 2- not the AvgLogFC, and we pressed the enter key.
#We created the column headers Control_Log_FC_Time and CHP_Log_FC_Time.
#We used the equation =SUMSQ(<range of cells for logFC_t0-2>)-COUNTA(<range of cells for logFC_t0-2>)*<AvgLogFC_t0-2>^2 and hit enter for each of the rows that were not the average.
#The amount of data points we have is: 21. Number of time points we have is: 7.
#We replaced <range of cells for logFC_0-2> with the data range associated with t15 and so on for each time point.
#We replaced <AvgCHPLogFC_0-2> and <AvgControlLogFC_0-2> with the cell number that we computed the AvgCHPLogFC and AvgControlLogFC for 0-2, and the "^2" squares that value. This was repeated for each of time points across our data set.
#We created the column headers CHP_SS_full and Control_SS_full.
#Below this, we used the formula: =sum(<range of cells containing "ss" for each timepoint>) and hit enter.
#In the next two columns to the right, we created the headers CHP_Fstat and Control_Fstat as well as CHP_p-value and Control_p-value.
#Since n=21 and t=7, in the first cell of each Fstat column, we used the formula =((21-7)/7)*(<CHP_ss_HO>-<CHP_SS_full>)/<CHP_SS_full>) and hit enter. This same process was repeated for the control.
#We replaced the phrase CHP_ss_HO with the cell designation and replaced the phrase <CHP_SS_full> with the cell designation. This was also repeated for the control.
#Below the CHP_p-value header, we used the formula =FDIST(<CHP_Fstat>,7,21-7) replacing the phrase <CHP_Fstat> with the cell designation. We used this same formula for the Control_p-value column.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 22:50, 17 April 2024 (PDT)
[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 13:59, 18 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

Data Analysts Week 13

2024-04-18T21:36:27Z

Ckapla12: adding formulas and working on procedure- fstat and p value

==Charlotte and Katie's Data Analyst Journal==

===Milestone 1===
Completed as of April 11th when we gave our Journal Club Presentation with [[User:Hivanson| Hailey Ivanson]]

===Milestone 2===
#With Quality Assurance team member [[User:Hivanson| Hailey Ivanson]], we downloaded and examined the microarray dataset: [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD Processed Data].
#We made a sample-data relationship table in Excel labeled "reorganized" that lists all of the samples and at which time point they were collected, and their replicate number. We came up with consistent column headers that summarize this information. We named each column either Control_LogFC_timepoint-replicatenumber or CHP_LogFC_timepoint-replicatenumber, as in Control_LogFC_0-1 and CHP_LogFC_0-1. The timepoint for each is either 0, 3 , 6, 12, 20, 40, 70, or 120, and the replicate number either 1, 2, or 3. We organized the data in a worksheet in an Excel workbook so that:
#*ID is the first column header, and within it are all of the SGD systemic names
#*Data columns are to the right, in increasing chronological order, using the column header pattern we created
#*Treatments are grouped together
#*Replicates are grouped together
#*We deleted the "EWEIGHT" row and "GWEIGHT" column.
#*We then had to undo the log-transformed raw intensity values. We first created new columns for each respective trial in the formats Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber, as in Control_FC_0-1 and CHP_FC_0-1. We then transformed the data in the first cell of each column with the equation <code>=2^<cell designation></code>, where the cell designation is the first cell of the respective Control_LogFC_timepoint-replicatenumber and CHP_LogFC_timepoint-replicatenumber columns, and then applied this command to the remaining cells of the column.
#*We then created a new worksheet labeled "with_averages", in which we copy and special pasted the values of the columns with headers Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber.
#*We then created new columns called Control_FC_0-avg and CHP_FC_0-avg to the right of their respective t0 timepoint trials, and then within them computed the average value of the t0 timepoint trials for the control and CHP-treated data. In the first cell below the column headed Control_FC_0-avg, we used the Excel command <code>=AVG(B2:D2)</code> and then applied this command to all cells in the column. In the first cell below the column headed CHP_FC_0-avg column, we used the command <code>=AVG(F2:H2)</code> and then applied this command to all cells in the column.
#*We then created new columns to the right of each treatment with a column header either Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Fold_Change_3-1 or CHP_Fold_Change_3-1. We then calculated the fold change by dividing the first cell of each trial by the average t0 value for the respective treatment (control or CHP-treated), and then applying this throughout the column. To the right of each new column, we also created created columns with a column header either Control_Log2_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Log2_Fold_Change_3-1 or CHP_Log2_Fold_Change_3-1. In each Log2 column, We then log2 transformed the fold changes by using <code>=LOG(cell designation, 2)</code>, where the cell designation is the first cell of the respective Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber columns. We then applied this throughout all of the cells in each Log2 column.

===Milestone 3===
#We created a new worksheet, naming it "CHP_ANOVA".
#We copied all the Control_Log2_Fold_Change_timepoint-replicatenumber and CHP_Log2_Fold_Change_timepoint-replicatenumber columns and special pasted only the values into the new worksheet.
#To the right of each group of either the Control or CHP replicates at one timepoint, we created columns with headers in the form Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint, where timepoint is either 3, 6, 12, 20, 40, 70, or 120.
# In the cell below the Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint headers, we typed =AVG(replicate 1 cell designation:replicate 3 cell designation), where the cell designations are the first cells of the replicate 1 at one timepoint and the replicate 3 at that same time point. This computed the average of replicate values, and we then applied this throughout the remaining cells in the column.
# To the right, we then copy and special pasted the values of each Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint columns. To the right of these, we created columns with the the headers Control_ss_HO and CHP_ss_HO.
#In the first cell below Control_ss_HO, we typed <code>=SUMSQ(B2,C2,D2,J2,K2,L2,R2,S2,T2,Z2,AA2,AB2,AH2,AI2,AJ2,AP2,AQ2,AR2,AX2,AY2,AZ2)</code> and clicked enter, and below CHP_ss_HO, we typed <code>=SUMSQ(F2,G2,H2,N2,O2,P2,V2,W2,X2,AD2,AE2,AF2,AL2,AM2,AN2,AT2,AU2,AV2,BB2,BC2,BD2)</code> and clicked enter.
#In the first cell below this header, we typed =SUMSQ for each of the time points.
#After this, we highlighted all of the LogFC data in row 2- not the AvgLogFC, and we pressed the enter key.
#We created the column headers Control_Log_FC_Time and CHP_Log_FC_Time.
#We used the equation =SUMSQ(<range of cells for logFC_t0-2>)-COUNTA(<range of cells for logFC_t0-2>)*<AvgLogFC_t0-2>^2 and hit enter for each of the rows that were not the average.
#The amount of data points we used is: ____
#We replaced <range of cells for logFC_0-2> with the data range associated with t15 and so on for each time point.
#We replaced <AvgCHPLogFC_0-2> and <AvgControlLogFC_0-2> with the cell number that we computed the AvgCHPLogFC and AvgControlLogFC for 0-2, and the "^2" squares that value. This was repeated for each of time points across our data set.
#We created the column headers CHP_SS_full and Control_SS_full.
#Below this, we used the formula: =sum(<range of cells containing "ss" for each timepoint>) and hit enter.
#In the next two columns to the right, we created the headers CHP_Fstat and Control_Fstat as well as CHP_p-value and Control_p-value.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 22:50, 17 April 2024 (PDT)
[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 13:59, 18 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

Data Analysts Week 13

2024-04-18T21:31:05Z

Ckapla12: writing procedure.

==Charlotte and Katie's Data Analyst Journal==

===Milestone 1===
Completed as of April 11th when we gave our Journal Club Presentation with [[User:Hivanson| Hailey Ivanson]]

===Milestone 2===
#With Quality Assurance team member [[User:Hivanson| Hailey Ivanson]], we downloaded and examined the microarray dataset: [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD Processed Data].
#We made a sample-data relationship table in Excel labeled "reorganized" that lists all of the samples and at which time point they were collected, and their replicate number. We came up with consistent column headers that summarize this information. We named each column either Control_LogFC_timepoint-replicatenumber or CHP_LogFC_timepoint-replicatenumber, as in Control_LogFC_0-1 and CHP_LogFC_0-1. The timepoint for each is either 0, 3 , 6, 12, 20, 40, 70, or 120, and the replicate number either 1, 2, or 3. We organized the data in a worksheet in an Excel workbook so that:
#*ID is the first column header, and within it are all of the SGD systemic names
#*Data columns are to the right, in increasing chronological order, using the column header pattern we created
#*Treatments are grouped together
#*Replicates are grouped together
#*We deleted the "EWEIGHT" row and "GWEIGHT" column.
#*We then had to undo the log-transformed raw intensity values. We first created new columns for each respective trial in the formats Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber, as in Control_FC_0-1 and CHP_FC_0-1. We then transformed the data in the first cell of each column with the equation <code>=2^<cell designation></code>, where the cell designation is the first cell of the respective Control_LogFC_timepoint-replicatenumber and CHP_LogFC_timepoint-replicatenumber columns, and then applied this command to the remaining cells of the column.
#*We then created a new worksheet labeled "with_averages", in which we copy and special pasted the values of the columns with headers Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber.
#*We then created new columns called Control_FC_0-avg and CHP_FC_0-avg to the right of their respective t0 timepoint trials, and then within them computed the average value of the t0 timepoint trials for the control and CHP-treated data. In the first cell below the column headed Control_FC_0-avg, we used the Excel command <code>=AVG(B2:D2)</code> and then applied this command to all cells in the column. In the first cell below the column headed CHP_FC_0-avg column, we used the command <code>=AVG(F2:H2)</code> and then applied this command to all cells in the column.
#*We then created new columns to the right of each treatment with a column header either Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Fold_Change_3-1 or CHP_Fold_Change_3-1. We then calculated the fold change by dividing the first cell of each trial by the average t0 value for the respective treatment (control or CHP-treated), and then applying this throughout the column. To the right of each new column, we also created created columns with a column header either Control_Log2_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Log2_Fold_Change_3-1 or CHP_Log2_Fold_Change_3-1. In each Log2 column, We then log2 transformed the fold changes by using <code>=LOG(cell designation, 2)</code>, where the cell designation is the first cell of the respective Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber columns. We then applied this throughout all of the cells in each Log2 column.

===Milestone 3===
#We created a new worksheet, naming it "CHP_ANOVA".
#We copied all the Control_Log2_Fold_Change_timepoint-replicatenumber and CHP_Log2_Fold_Change_timepoint-replicatenumber columns and special pasted only the values into the new worksheet.
#To the right of each group of either the Control or CHP replicates at one timepoint, we created columns with headers in the form Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint, where timepoint is either 3, 6, 12, 20, 40, 70, or 120.
# In the cell below the Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint headers, we typed =AVG(replicate 1 cell designation:replicate 3 cell designation), where the cell designations are the first cells of the replicate 1 at one timepoint and the replicate 3 at that same time point. This computed the average of replicate values, and we then applied this throughout the remaining cells in the column.
# To the right, we then copy and special pasted the values of each Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint columns. To the right of these, we created columns with the the headers Control_ss_HO and CHP_ss_HO.
#In the first cell below Control_ss_HO, we typed <code>=SUMSQ(B2,C2,D2,J2,K2,L2,R2,S2,T2,Z2,AA2,AB2,AH2,AI2,AJ2,AP2,AQ2,AR2,AX2,AY2,AZ2)</code> and clicked enter, and below CHP_ss_HO, we typed <code>=SUMSQ(F2,G2,H2,N2,O2,P2,V2,W2,X2,AD2,AE2,AF2,AL2,AM2,AN2,AT2,AU2,AV2,BB2,BC2,BD2)</code> and clicked enter.
#In the first cell below this header, we typed =SUMSQ for each of the time points.
#After this, we highlighted all of the LogFC data in row 2- not the AvgLogFC, and we pressed the enter key.
#We created the column headers Control_Log_FC_Time and CHP_Log_FC_Time.
#We used the equation =SUMSQ(<range of cells for logFC_t0-2>)-COUNTA(<range of cells for logFC_t0-2>)*<AvgLogFC_t0-2>^2 and hit enter for each of the rows that were not the average.
#The amount of data points we used is: ____
#We replaced <range of cells for logFC_0-2> with the data range associated with t15 and so on for each time point.
#We replaced <AvgCHPLogFC_0-2> and <AvgControlLogFC_0-2> with the cell number that we computed the AvgCHPLogFC and AvgControlLogFC for 0-2, and the "^2" squares that value. This was repeated for each of time points across our data set.

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 22:50, 17 April 2024 (PDT)
[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 13:59, 18 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13

Data Analysts Week 13

2024-04-18T21:23:55Z

Ckapla12: adding data points to fill in later

==Charlotte and Katie's Data Analyst Journal==

===Milestone 1===
Completed as of April 11th when we gave our Journal Club Presentation with [[User:Hivanson| Hailey Ivanson]]

===Milestone 2===
#With Quality Assurance team member [[User:Hivanson| Hailey Ivanson]], we downloaded and examined the microarray dataset: [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD Processed Data].
#We made a sample-data relationship table in Excel labeled "reorganized" that lists all of the samples and at which time point they were collected, and their replicate number. We came up with consistent column headers that summarize this information. We named each column either Control_LogFC_timepoint-replicatenumber or CHP_LogFC_timepoint-replicatenumber, as in Control_LogFC_0-1 and CHP_LogFC_0-1. The timepoint for each is either 0, 3 , 6, 12, 20, 40, 70, or 120, and the replicate number either 1, 2, or 3. We organized the data in a worksheet in an Excel workbook so that:
#*ID is the first column header, and within it are all of the SGD systemic names
#*Data columns are to the right, in increasing chronological order, using the column header pattern we created
#*Treatments are grouped together
#*Replicates are grouped together
#*We deleted the "EWEIGHT" row and "GWEIGHT" column.
#*We then had to undo the log-transformed raw intensity values. We first created new columns for each respective trial in the formats Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber, as in Control_FC_0-1 and CHP_FC_0-1. We then transformed the data in the first cell of each column with the equation <code>=2^<cell designation></code>, where the cell designation is the first cell of the respective Control_LogFC_timepoint-replicatenumber and CHP_LogFC_timepoint-replicatenumber columns, and then applied this command to the remaining cells of the column.
#*We then created a new worksheet labeled "with_averages", in which we copy and special pasted the values of the columns with headers Control_FC_timepoint-replicatenumber and CHP_FC_timepoint-replicatenumber.
#*We then created new columns called Control_FC_0-avg and CHP_FC_0-avg to the right of their respective t0 timepoint trials, and then within them computed the average value of the t0 timepoint trials for the control and CHP-treated data. In the first cell below the column headed Control_FC_0-avg, we used the Excel command <code>=AVG(B2:D2)</code> and then applied this command to all cells in the column. In the first cell below the column headed CHP_FC_0-avg column, we used the command <code>=AVG(F2:H2)</code> and then applied this command to all cells in the column.
#*We then created new columns to the right of each treatment with a column header either Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Fold_Change_3-1 or CHP_Fold_Change_3-1. We then calculated the fold change by dividing the first cell of each trial by the average t0 value for the respective treatment (control or CHP-treated), and then applying this throughout the column. To the right of each new column, we also created created columns with a column header either Control_Log2_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber, as in Control_Log2_Fold_Change_3-1 or CHP_Log2_Fold_Change_3-1. In each Log2 column, We then log2 transformed the fold changes by using <code>=LOG(cell designation, 2)</code>, where the cell designation is the first cell of the respective Control_Fold_Change_timepoint-replicatenumber or CHP_Fold_Change_timepoint-replicatenumber columns. We then applied this throughout all of the cells in each Log2 column.

===Milestone 3===
#We created a new worksheet, naming it "CHP_ANOVA".
#We copied all the Control_Log2_Fold_Change_timepoint-replicatenumber and CHP_Log2_Fold_Change_timepoint-replicatenumber columns and special pasted only the values into the new worksheet.
#To the right of each group of either the Control or CHP replicates at one timepoint, we created columns with headers in the form Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint, where timepoint is either 3, 6, 12, 20, 40, 70, or 120.
# In the cell below the Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint headers, we typed =AVG(replicate 1 cell designation:replicate 3 cell designation), where the cell designations are the first cells of the replicate 1 at one timepoint and the replicate 3 at that same time point. This computed the average of replicate values, and we then applied this throughout the remaining cells in the column.
# To the right, we then copy and special pasted the values of each Avg_Control_Log_FC_timepoint or Avg_CHP_Log_FC_timepoint columns. To the right of these, we created columns with the the headers Control_ss_HO and CHP_ss_HO.
#In the first cell below Control_ss_HO, we typed <code>=SUMSQ(B2,C2,D2,J2,K2,L2,R2,S2,T2,Z2,AA2,AB2,AH2,AI2,AJ2,AP2,AQ2,AR2,AX2,AY2,AZ2)</code> and clicked enter, and below CHP_ss_HO, we typed <code>=SUMSQ(F2,G2,H2,N2,O2,P2,V2,W2,X2,AD2,AE2,AF2,AL2,AM2,AN2,AT2,AU2,AV2,BB2,BC2,BD2)</code> and clicked enter.
#In the first cell below this header, we typed =SUMSQ for each of the time points.
#After this, we highlighted all of the LogFC data in row 2- not the AvgLogFC, and we pressed the enter key.
#We created the column headers Control_Log_FC_Time and CHP_Log_FC_Time.
#We used the equation =SUMSQ(<range of cells for logFC_t15>)-COUNTA(<range of cells for logFC_t15>)*<AvgLogFC_t15>^2 and hit enter for each of the rows that were not the average.
#The amount of data points we used is: ____

==Acknowledgements==
This procedure was adapted from the Data Analysis page Milestone 1, 2, and 3 protocols, linked here: [[Data Analysis]]
The procedure for Milestone 3 was also adapted from the steps outlined in the Week 9 assignment page.

Except for what is noted above, this individual journal entry was completed by Katie and Charlotte and not copied from another source.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 22:50, 17 April 2024 (PDT)
[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 13:59, 18 April 2024 (PDT)

==References==
LMU BioDB 2024. (2024). Week 13. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_13