Difference between revisions of "Knguye66 Eyoung20 Week 12/13"
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#* 677, 15.2% | #* 677, 15.2% | ||
| − | # | + | # Microarray data was prepared to be loaded into the STEM software |
| − | #* | + | #* A new worksheet was added into the Excel workbook, and named "Thiuram_stem". |
| − | #* | + | #* Then all of the data from your "Thiuram_ANOVA" worksheet was Paste special > paste values into the "Thiuram_stem" worksheet. |
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name". | #** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name". | ||
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case). | #** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case). | ||
Revision as of 14:43, 21 November 2019
Combined Individual Journals for Kaitlyn Nguyen and Emma Young (Data Analysts).
Contents
Purpose
The purpose of this assignment is to record our progress towards the FunGals group deliverables as the Data Analysts for this week and the future weeks to come.
Methods and Results: Progress
Progress 11/21/19
- Our group decided to have the ANOVA, sanity check, and STEM set-up done before class on Thursday, 11/21/19
- First created a worksheet and labeled accordingly based on the format the Coder's Guild decided
- Finished the steps on Week 8 for Statistical Analysis Part I: ANOVA on Microsoft Excel for the new MicroArray Data found on the Data Analysis page
- For questions asked on the p-value (use: "out of 4468" genes instead of "out of 6189" to adjust for this data)
- Following the ANOVA: Part I, Bonferroni, Benjamini & Hochberg, and p-value correction, a quick sanity check was performed for the p-value dataset.
Sanity Check Questions:
-Unadjusted p-value-
- How many genes have p<0.05? and what is the percentage (out of 4468)?
- 1196
- How many genes have p<0.01? and what is the percentage (out of 4468)?
- 731
- How any genes have p<0.001? and what is the percentage (out of 4468)?
- 380
- How many genes have p<0.0001? and what is the percentage (out of 4468)?
- 190
-Bonferroni & Benjamini and Hochberg p-value-
- How many genes are p<0.05 for the Bonferroni-corrected p-value? and what is the percentage (out of 4468)?
- 103, 2.3%
- How many genes are p <0.05 for the Benjamini and Hochberg-corrected p-value? and what is the percentage (out of 4468)?
- 677, 15.2%
- Microarray data was prepared to be loaded into the STEM software
- A new worksheet was added into the Excel workbook, and named "Thiuram_stem".
- Then all of the data from your "Thiuram_ANOVA" worksheet was Paste special > paste values into the "Thiuram_stem" worksheet.
- Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
- Filter the data on the B-H corrected p value to be > 0.05 (that's greater than in this case).
- Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.
- Delete all of the data columns EXCEPT for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
- Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
- Save your work. Then use Save As to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
- Note that you should turn on the file extensions if you have not already done so.
- Now download and extract the STEM software. Click here to go to the STEM web site.
Conclusion
The first stage of our group's project was completed via referencing Week 8 and using Microsoft Excel to complete the tasks. The excel file will be located in the FunGals page for viewing and download.
Acknowledgements
This section is in acknowledgement to partner Kaitlyn Nguyen (User:knguye66), Michael Armas (User:Marmas), as well as, Iliana Crespin (User:Icrespin), and Emma Young (User:eyoung20). We would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment.
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Knguye66 (talk) 18:49, 20 November 2019 (PST)
References
- Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
- Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
- Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
- Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
User Page
User:knguye66
Template Page
Template:knguye66
