Mavila9 Week 8 - Revision history

Mavila9: /* Data */ image

2019-10-24T22:27:30Z

‎Data: image

Mavila9: /* Data */ sanity check

2019-10-24T21:22:05Z

‎Data: sanity check

Mavila9: /* Calculating the Bonferroni and p value Correction */

2019-10-23T22:07:21Z

‎Calculating the Bonferroni and p value Correction

Mavila9: /* Purpose */ fix

2019-10-23T21:42:29Z

‎Purpose: fix

Mavila9: /* Methods & Results */

2019-10-23T21:40:09Z

‎Methods & Results

Mavila9: /* Calculating the Benjamini & Hochberg p value Correction */

2019-10-23T21:39:33Z

‎Calculating the Benjamini & Hochberg p value Correction

Mavila9: /* Data */ add slide

2019-10-23T21:37:15Z

‎Data: add slide

Mavila9: /* Data */ add txt

2019-10-23T21:34:27Z

‎Data: add txt

Mavila9: /* Conclusion */ add

2019-10-23T21:31:42Z

‎Conclusion: add

Mavila9: /* Sanity Check: Number of genes significantly changed */

2019-10-23T21:29:02Z

‎Sanity Check: Number of genes significantly changed

← Older revision		Revision as of 22:27, 24 October 2019
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	[[media:BIOL367 F19 wt p-value slide mavila9.zip \| Sanity Check Table]]		[[media:BIOL367 F19 wt p-value slide mavila9.zip \| Sanity Check Table]]
		+
		+	[[image:Stem results1.JPG]]

	== Conclusion ==		== Conclusion ==

@@ Line 105: / Line 105: @@
 [[media:BIOL367 F19 microarray-data wtMAVILA9 Benjamini^0Hochberg Pvalue Correction.txt | Microarray Data .txt]]
-[[media:BIOL367 F19 wt p-value slide mavila9.zip]]
+[[media:BIOL367 F19 wt p-value slide mavila9.zip | Sanity Check Table]]
 == Conclusion ==

@@ Line 41: / Line 41: @@
 #* Any filters that were applied were removed before making any additional calculations.
-==== Calculating the Bonferroni and p value Correction ====
+==== Calculating the Bonferroni and p-value Correction ====
 # The next two columns to the right were labeled with the same label, wt_Bonferroni_p-value.

@@ Line 3: / Line 3: @@
 == Purpose ==
-This investigation was done to analyze the data of the life cycle for a DNA microarray dataset and develop knowledge about what different p-value cut-offs mean.
+This investigation was done to analyze the microarray data to determine changes in gene expression after a cold shock.
 == Methods & Results ==

← Older revision		Revision as of 21:40, 23 October 2019
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	==== ANOVA: Part 1 ====		==== ANOVA: Part 1 ====
−
−	~~The purpose of the within-stain ANOVA test is to determine if any genes had a gene expression change that was significantly different than zero at '''''any''''' timepoint.~~

	# A new worksheet was created named "wt_ANOVA".		# A new worksheet was created named "wt_ANOVA".

@@ Line 56: / Line 56: @@
 # Columns A, B, C, and D were selected and sorted by ascending values on Column D. The sort button was clicked on the toolbar, and in the window that appears column D was sorted from smallest to largest.
 # "Rank" was typed in the cell E1. "1" was typed into cell E2 and "2" into cell E3. Both cells E2 and E3 were selected then the plus sign in the lower right-corner was double-clicked to fill the column with a series of numbers from 1 to 6189.
-# The Benjamini and Hochberg p-value correction was calculated next. wt_B-H_p-value was typed into cell F1. The following formula was typed into cell F2: <code>=(D2*6189)/E2</code> and enter was press. That equation was copied throughout the entire column.
+# The Benjamini and Hochberg p-value correction was calculated next. "wt_B-H_p-value" was typed into cell F1. The following formula was typed into cell F2: <code>=(D2*6189)/E2</code> and enter was press. That equation was copied throughout the entire column.
 # "STRAIN_B-H_p-value" was typed into cell G1.
 # The following formula was typed into cell G2: <code>=IF(F2>1,1,F2)</code> and enter was press. That equation was copied throughout the entire column.

← Older revision		Revision as of 21:37, 23 October 2019
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	[[media:BIOL367 F19 microarray-data wtMAVILA9 Benjamini^0Hochberg Pvalue Correction.txt \| Microarray Data .txt]]		[[media:BIOL367 F19 microarray-data wtMAVILA9 Benjamini^0Hochberg Pvalue Correction.txt \| Microarray Data .txt]]
		+
		+	[[media:BIOL367 F19 wt p-value slide mavila9.zip]]

	== Conclusion ==		== Conclusion ==

@@ Line 103: / Line 103: @@
 == Data ==
-[[media:BIOL367 F19 microarray-data wtMAVILA9 Benjamini&Hochberg Pvalue Correction.zip | Microarray Data]]
+[[media:BIOL367 F19 microarray-data wtMAVILA9 Benjamini&Hochberg Pvalue Correction.zip | Microarray Data .zip]]
 == Conclusion ==

@@ Line 107: / Line 107: @@
 == Conclusion ==
-In conclusion, the wild type p-values were calculated for each gene allowing statistical significance to be determined. Next Bonferroni and Benjamini & Hochberg p-value adjustments were done to correct for the multiple testing problem.
+In conclusion, the wild type p-values were calculated for each gene allowing statistical significance to be determined. Next Bonferroni and Benjamini & Hochberg p-value adjustments were done to correct for the multiple testing problem. The microarray data was prepared to be run on the STEM program.
 == Acknowledgements ==

@@ Line 71: / Line 71: @@
 * To see the relationship of the less stringent Benjamini-Hochberg correction the data was filtered to determine: how many genes are p < 0.05 for the Bonferroni-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)?
 * The numbers were organized as a table using this [[Media:BIOL367_F19_sample_p-value_slide.pptx | sample PowerPoint slide]] then compared to other strains after the slide was uploaded to the wiki.
-* Comparing results with known data: the expression of the gene ''NSR1'' (ID: YGR159C) is known to be induced by cold shock, so the unadjusted, Bonferroni-corrected, and B-H-corrected p values were found of this gene, along with it's average Log fold change at each of the timepoints in the experiment to determine whether ''NSR1'' changed expression due to cold shock.
+* Comparing results with known data: the expression of the gene NSR1 (ID: YGR159C) is known to be induced by cold shock, so the unadjusted, Bonferroni-corrected, and B-H-corrected p values were found of this gene, along with it's average Log fold change at each of the timepoints in the experiment to determine whether ''NSR1'' changed expression due to cold shock.
 * The unadjusted, Bonferroni-corrected, and B-H-corrected p values for the gene YBR160W/CDC28 in the dataset were found along with the average Log fold change at each of the timepoints in the experimentto determine whether gene expression changed due to cold shock.