Hivanson Week 15 - Revision history

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ yeastract tool

2024-05-03T18:03:31Z

‎Electronic laboratory notebook for weeks 14-15: yeastract tool

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ some more info on expression table and more detail on the presentation contributions

2024-05-03T17:50:41Z

‎Electronic laboratory notebook for weeks 14-15: some more info on expression table and more detail on the presentation contributions

Hivanson: /* References */ added data analysts week 14

2024-05-03T17:36:40Z

‎References: added data analysts week 14

Hivanson: /* Acknowledgments */ refs actually

2024-05-03T17:36:10Z

‎Acknowledgments: refs actually

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ acknowledgments

2024-05-03T17:28:23Z

‎Electronic laboratory notebook for weeks 14-15: acknowledgments

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ steps outlined

2024-05-03T17:19:43Z

‎Electronic laboratory notebook for weeks 14-15: steps outlined

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ refs

2024-05-03T17:18:30Z

‎Electronic laboratory notebook for weeks 14-15: refs

Hivanson: templates

2024-05-03T17:17:09Z

templates

Hivanson: /* Electronic laboratory notebook for weeks 14-15 */ for presentation

2024-05-03T17:16:39Z

‎Electronic laboratory notebook for weeks 14-15: for presentation

Hivanson: header and filling for journal

2024-05-03T17:10:03Z

header and filling for journal

@@ Line 3: / Line 3: @@
 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 helped Charlotte and Katie run the Stem analysis. Steps outlined [[Data_Analysts_Week_14|here]].

@@ Line 1: / Line 1: @@
 ===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 [[Data_Analysts_Week_14|here]]. 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 outlined [[Data_Analysts_Week_14|here]].
@@ Line 8: / Line 8: @@
 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, 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.

@@ Line 22: / Line 22: @@
 ===References===
 *LMU BioDB 2024. (2024). Data Analysis. Retrieved May 3, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Data_Analysis
 *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

@@ Line 20: / Line 20: @@
 [[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 10:28, 3 May 2024 (PDT)
 {{Yeast Beasts}}
 {{Hivanson}}

@@ Line 11: / Line 11: @@
 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.
 {{Yeast Beasts}}
 {{Hivanson}}

← Older revision		Revision as of 17:17, 3 May 2024
Line 9:		Line 9:

	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, 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.
		+
		+	{{Yeast Beasts}}
		+	{{Hivanson}}

@@ Line 2: / Line 2: @@
 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 made the expression table to send to the coder/designers.
-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 and the sanity check values were readjusted for the CHP data.
 I helped Charlotte and Katie run the Stem analysis. Steps outlines [[somewhere]]
 I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.

← Older revision		Revision as of 17:10, 3 May 2024
Line 1:		Line 1:
−	[[~~Media:~~~~~$Yeast_Beasts_Presentation_(1~~).~~pptx~~.~~zip~~]]	+	===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 on [[somewhere]]. I ran the sanity check to find the ideal B&H p-value (significance of ~25%).
		+	I made the expression table to send to the coder/designers.
		+	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.
		+
		+	I helped Charlotte and Katie run the Stem analysis. Steps outlines [[somewhere]]
		+
		+	I used GRNsight using the first 23 most significant transcription factors from profile 41 from Yeastract. This was not used in the final project.