Ckaplan Week 9 - Revision history

Ckapla12: updated p values

2024-03-24T22:20:47Z

updated p values

2024-03-24T22:13:04Z

putting in updated file

2024-03-21T06:36:45Z

spelling mistake

2024-03-21T06:14:39Z

grammar error

2024-03-21T06:12:40Z

uploading table

2024-03-21T06:09:07Z

References, acknowledgements, signature

2024-03-21T06:02:09Z

favorite gene values- sir2

2024-03-21T05:59:48Z

cold shock question

2024-03-21T05:58:49Z

analyzing nsir

2024-03-21T05:55:29Z

answers

← Older revision		Revision as of 22:20, 24 March 2024
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	[[Media:Untitled_presentation.pdf]]		[[Media:Untitled_presentation.pdf]]
		+
		+	[[Media:Updated_Pvalues_ckaplan.pdf]]

	===Procedure:===		===Procedure:===

← Older revision		Revision as of 22:13, 24 March 2024
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	[[Media:BIOL367_S24_microarray-data_dGLN3CKAS3121.xlsx]].		[[Media:BIOL367_S24_microarray-data_dGLN3CKAS3121.xlsx]].
		+
		+	[[Media: BIOL367_S24_microarray-data_dGLN3CKAS31211.xlsx]]

	[[Media:Untitled_presentation.pdf]]		[[Media:Untitled_presentation.pdf]]

@@ Line 60: / Line 60: @@
 There may be an issue with the data as the number of rows seem un proportionate.
-Analyzing nsir in the data:
+Analyzing nsr1 in the data:
 -Unadjusted P-value 0.000506764
 -Bonferroni p-value 3.136364678
 -B&H value of 1.
 -Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.
-*I don't think nsir changes with cold shock.
+*I don't think nsr1 changes with cold shock.
 -Favorite gene: Sir2

@@ Line 1: / Line 1: @@
 ===Purpose:===
-We're utilizing Excel to practice loading data and conducting statistical analysis specifically on the gene expression data of the "Δgln3" strain. This exercise helps us refine our skills in organizing interpreting biological data.
+We're utilizing Excel to practice loading data and conducting statistical analysis specifically on the gene expression data of the "Δgln3" strain. This exercise helps us refine our skills in organizing and interpreting biological data.
 ===Methods:===

← Older revision		Revision as of 06:12, 21 March 2024
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	[[Media:BIOL367_S24_microarray-data_dGLN3CKAS3121.xlsx]].		[[Media:BIOL367_S24_microarray-data_dGLN3CKAS3121.xlsx]].
		+
		+	[[Media:Untitled_presentation.pdf]]

	===Procedure:===		===Procedure:===

← Older revision		Revision as of 06:09, 21 March 2024
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	Log fold changes ranging from t15, t30, t60, t90, t120: 0.50352, 0.578, 0.60005, -0.07517, -0.168375.		Log fold changes ranging from t15, t30, t60, t90, t120: 0.50352, 0.578, 0.60005, -0.07517, -0.168375.

		+	===Conclusion:===
		+	After speaking with Andrew, we both concluded that there may be an issue with the data as the number of rows seem un proportionate. Bonferroni had more data than Benjamini and Hochberg. We are going to speak with Dr. Dahlquist in class tomorrow for clarification.

		+	===References:===
		+
		+	Dahlquist, K. Master_sheet_dGLN3.
		+
		+	LMU BioDB 2024. (2024). Week 9. Retrieved Mar 20, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_9
		+
		+	===Acknowledgements:===
		+	I worked with my homework partner, Andrew Sandler, inside and outside of class. Andrew helped me keep up and catch up in class with the Excel since he has experience from his entrepreneurship degree. After completing this week's assignment, we communicated that we both may have gotten incorrect values for a certain section.
		+
		+	[[User:Ckapla12\|Ckapla12]] ([[User talk:Ckapla12\|talk]]) 23:09, 20 March 2024 (PDT) Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

← Older revision		Revision as of 06:02, 21 March 2024
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	-Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.		-Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.
	*I don't think nsir changes with cold shock.		*I don't think nsir changes with cold shock.
		+
		+	-Favorite gene: Sir2
		+	P-value of 0.01541894, Bonferroni p-value of 95.427866, and Benjamin and Hochberg correct value of 1.
		+	Log fold changes ranging from t15, t30, t60, t90, t120: 0.50352, 0.578, 0.60005, -0.07517, -0.168375.
		+
		+

← Older revision		Revision as of 05:59, 21 March 2024
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	-B&H value of 1.		-B&H value of 1.
	-Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.		-Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.
		+	*I don't think nsir changes with cold shock.

← Older revision		Revision as of 05:58, 21 March 2024
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	How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?		How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
	There may be an issue with the data as the number of rows seem un proportionate.		There may be an issue with the data as the number of rows seem un proportionate.
		+
		+	Analyzing nsir in the data:
		+	-Unadjusted P-value 0.000506764
		+	-Bonferroni p-value 3.136364678
		+	-B&H value of 1.
		+	-Log fold changes in increments of 15, 30, 60, 90, 120: 3.50622, 4.532, 2.759,-1.8502, -1.86742.

← Older revision		Revision as of 05:55, 21 March 2024
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	How many genes have p < 0.0001? and what is the percentage (out of 6189)?		How many genes have p < 0.0001? and what is the percentage (out of 6189)?
	180		180
		+
		+	How many genes are p < 0.05 for the Bonferroni-corrected p value? and what is the percentage (out of 6189)?
		+	There may be an issue with the data as the number of rows seem un proportionate. Bonferroni had more data than Benjamini and Hochberg
		+
		+	How many genes are p < 0.05 for the Benjamini and Hochberg-corrected p value? and what is the percentage (out of 6189)?
		+	There may be an issue with the data as the number of rows seem un proportionate.