Difference between revisions of "Hivanson Week 15"

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(→‎Electronic laboratory notebook for weeks 14-15: for presentation)
(→‎Electronic laboratory notebook for weeks 14-15: yeastract tool)
 
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===Electronic laboratory notebook for weeks 14-15===
 
===Electronic laboratory notebook for weeks 14-15===
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I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out on [[somewhere]]. I ran the sanity check to find the ideal B&H p-value (significance of ~25%).  
+
I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out [[Data_Analysts_Week_14|here]]. I ran the sanity check to find the ideal B&H p-value (goal: significance of ~25%).  
−
I made the expression table to send to the coder/designers.
+
I made the expression table to send to the coder/designers. There are two sheets in the expression table, each containing ONLY the ID in column 1, and Log2 Fold Change data for EITHER control OR CHP at each timepoint for each trial.
−
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated and the sanity check values were readjusted for the CHP data.
+
An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated by adding in the proper data to the ANOVA sheet, and re-running the Bonferroni and B&H corrections. The sanity check values were readjusted for the CHP data.
  
−
I helped Charlotte and Katie run the Stem analysis. Steps outlines [[somewhere]]
+
I also used the "ORF List <-> Gene List" tool at YEASTRACT to get the standard names for the significant genes in profile 41. This tool was also used to determine whether the transcription factors were part of our GRNmap cluster (Katie did this, but I converted the gene names).
 +
 
 +
I helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].
  
 
I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.
 
I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.
  
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For the final presentation, I made the flow chart, the outline, the Sha et al. background, put together and interpreted the GRNmaps, and drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.
+
For the final presentation, I made the flow chart using Goodnotes5, I made the outline, I wrote the Sha et al. background, I put together and interpreted the GRNmaps from what Dr. Dahlquist sent us, and I drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.
 +
 
 +
For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.
 +
 
 +
===Acknowledgments===
 +
I worked closely with [[User:Kmill104|Katie]] and [[User:Ckapla12|Charlotte]], the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The [[Yeast_Beasts|whole team]] communicated via text, call, FaceTime, and in person to work on the final presentation and paper.
 +
 
 +
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
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 +
 
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[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)
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===References===
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*LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
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*LMU BioDB 2024. (2024). Data Analysts Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_14
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*LMU BioDB 2024. (2024). Data Analysts Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysts_Week_15
 +
*LMU BioDB 2024. (2024). Week 9. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_9
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*LMU BioDB 2024. (2024). Week 10. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_10
 +
*LMU BioDB 2024. (2024). Week 14. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_14
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*LMU BioDB 2024. (2024). Week 15. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_15
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{{Yeast Beasts}}
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{{Hivanson}}

Latest revision as of 10:03, 3 May 2024

Electronic laboratory notebook for weeks 14-15

I helped Katie and Charlotte with generating the Bonferroni and B&H p-values. All of us worked on a shared Excel file to complete the work. Steps laid out here. I ran the sanity check to find the ideal B&H p-value (goal: significance of ~25%). I made the expression table to send to the coder/designers. There are two sheets in the expression table, each containing ONLY the ID in column 1, and Log2 Fold Change data for EITHER control OR CHP at each timepoint for each trial. An error that was encountered when sending the expression table was that I accidentally copy-pasted CHP data for timepoint 6 trial 2 into the spot for CHP timepoint 6 trial 3. This was present in the ANOVA Excel, too. This was quickly ameliorated by adding in the proper data to the ANOVA sheet, and re-running the Bonferroni and B&H corrections. The sanity check values were readjusted for the CHP data.

I also used the "ORF List <-> Gene List" tool at YEASTRACT to get the standard names for the significant genes in profile 41. This tool was also used to determine whether the transcription factors were part of our GRNmap cluster (Katie did this, but I converted the gene names).

I helped Charlotte and Katie run the Stem analysis. Steps outlined here.

I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

For the final presentation, I made the flow chart using Goodnotes5, I made the outline, I wrote the Sha et al. background, I put together and interpreted the GRNmaps from what Dr. Dahlquist sent us, and I drew the comparisons from our data to that of Sha et al. I also helped work on the future directions and conclusion, and finalized the references list.

For the final paper, I wrote the introduction, added figure captions to some of the Data Analysts section, helped with the conclusion, and imported and updated the references.

Acknowledgments

I worked closely with Katie and Charlotte, the Data Analysts, these past few weeks during class and in person to complete the rest of the data analyst's sections as well as all of the final deliverables. The whole team communicated via text, call, FaceTime, and in person to work on the final presentation and paper.

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


Hivanson (talk) 10:28, 3 May 2024 (PDT)

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