MSymond1 Week 9 - Revision history

Msymond1: /* Benjamini & Hochberg p-value correction */ pasted the protocol

2024-04-03T05:19:54Z

‎Benjamini & Hochberg p-value correction: pasted the protocol

2024-04-03T04:49:42Z

‎Bonferroni and p-value correction: copied protocol from assignment

2024-04-03T04:42:05Z

‎ANOVA: copied the protocol from the assignment

2024-04-03T04:04:21Z

‎Sanity Check: Fixed B-H p value

2024-03-21T04:23:27Z

references

2024-03-21T04:21:14Z

added acknowledgements

2024-03-21T04:15:21Z

finished conclusion

2024-03-21T04:01:20Z

‎Data & Files: added slide

2024-03-21T03:59:40Z

added excel workbook

2024-03-21T03:50:43Z

‎Sanity Check: finished sanity check

@@ Line 45: / Line 45: @@
 ===Benjamini & Hochberg p-value correction===
-A new worksheet was created in Excel with all of the raw p-values, the p-values were ranked from least to greatest in this new worksheet. To calculate the new p-values, the p-values were multiplied by 6189 again, and then they were divided by their rank of the p-values. The same process was repeated from the Bonferroni calculations in which they were only reported if they were less than 1.
+# a new worksheet was inserted, named "(STRAIN)_ANOVA_B-H".
 ===Sanity Check===
 #NSR1

@@ Line 39: / Line 39: @@
 ===Bonferroni and p-value correction===
-To calculate the Bonferroni p-value, the original p values were all multiplied by 6189. Then, in another column, the Bonferroni p values were all either changed to 1 if they were greater than 1, or they were reported as their Bonferroni p-values if they were less than 1.
+''any filters that have been applied were undone before continuing with the next steps.''
 ===Benjamini & Hochberg p-value correction===
 A new worksheet was created in Excel with all of the raw p-values, the p-values were ranked from least to greatest in this new worksheet. To calculate the new p-values, the p-values were multiplied by 6189 again, and then they were divided by their rank of the p-values. The same process was repeated from the Bonferroni calculations in which they were only reported if they were less than 1.

@@ Line 3: / Line 3: @@
 ==Methods & Results==
 ===ANOVA===
-The data was imported into Microsoft Excel, an ANOVA test was run on every gene (6189) in the data set by first calculating the average of each data point for each time interval (15, 30, 60, 90, 120). Then the sum of squares for each time interval was also calculated using the syntax provided by the lab protocol. The Fstat was then calculated for the full dataset, which then allowed to calculate the p-value for each gene. Once the p-values were all calculated, they were then modified to correct for the multiple testing problem.
+# A new worksheet was created, named "(STRAIN)_ANOVA" as appropriate.  For example, you might call yours "wt_ANOVA" or "dCIN5_ANOVA".
 ===Bonferroni and p-value correction===
 To calculate the Bonferroni p-value, the original p values were all multiplied by 6189. Then, in another column, the Bonferroni p values were all either changed to 1 if they were greater than 1, or they were reported as their Bonferroni p-values if they were less than 1.

@@ Line 12: / Line 12: @@
 #*Unadjusted p-value: 2.86939E-10
 #*Bonferroni p-value: 1.77586E-06
-#*B-H p-value: 0.111519036
+#*B-H p-value: 8.87931530097403E-07
 #*Average log
 #**15: 3.279225

@@ Line 42: / Line 42: @@
 I worked with my homework partner, Katie Miller during class as our professor, Dr. Dahlquist showed us the protocol for how to run the tests on the database in Excel. I did not communicate with Katie or Dr. Dahlquist outside of class for the assignment. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 21:21, 20 March 2024 (PDT)
 {{Template:MSymond1}}

@@ Line 38: / Line 38: @@
 ==Conclusion==
 This experiment gives many implications to the viability of using p-values from ANOVA tests. Several of the p values that came out as less than .05 from the ANOVA test did not have a p-value of less than .05 for the Bonferroni test or the B-H test. Not to mention that the p-value being less than .05 is an arbitrary comparison to begin with. With a sample size this large, it is very important to understand that there will be many times the p values seem to indicate a significant result when there in fact is not one. The Bonferroni tests and B-H tests also yielded far less p values that were less than .05. It is very interesting that this has such large implications for the field of biology and most of the sciences, but this has never been taught to the experimenter before in this study.
 {{Template:MSymond1}}

← Older revision		Revision as of 04:01, 21 March 2024
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	===Data & Files===		===Data & Files===
	[[media:Symonds_Miller_BIOL367_S24_microarray-data_wt.xlsx.zip]]		[[media:Symonds_Miller_BIOL367_S24_microarray-data_wt.xlsx.zip]]
		+	[[media:Symonds_BIOL367_S24_sample_p-value_slide.pdf]]

← Older revision		Revision as of 03:59, 21 March 2024
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	#**120: -0.18418		#**120: -0.18418
	#*According to all 3 p-values, it does not undergo change in expression during the experiment.		#*According to all 3 p-values, it does not undergo change in expression during the experiment.
		+
		+	===Data & Files===
		+	[[media:Symonds_Miller_BIOL367_S24_microarray-data_wt.xlsx.zip]]

@@ Line 19: / Line 19: @@
 #**90: -2.04985
 #**120: -0.60622
 #MSN1
 #*Unadjusted p-value: 0.563798852
@@ Line 29: / Line 30: @@
 #**90: 0.16805
 #**120: -0.18418