QLanners Week 8 - Revision history

Qlanners: small typo fixed

2017-10-24T05:13:53Z

small typo fixed

Qlanners: small typo fixed

2017-10-24T05:12:22Z

small typo fixed

Qlanners: small edit to general information

2017-10-23T00:35:34Z

small edit to general information

Qlanners: edited acknowledgements

2017-10-23T00:30:56Z

edited acknowledgements

Qlanners: added to acknowledgements

2017-10-20T04:42:29Z

added to acknowledgements

Qlanners: added acknowledgements and references

2017-10-20T04:40:33Z

added acknowledgements and references

Qlanners: added pptx table and summary paragraph

2017-10-20T04:32:05Z

added pptx table and summary paragraph

Qlanners: finished the electronic journal

2017-10-20T04:01:26Z

finished the electronic journal

Show changes

Qlanners: added electronic journal

2017-10-20T03:37:24Z

added electronic journal

Show changes

Qlanners: added information on p values and NSR1 gene

2017-10-20T03:10:14Z

added information on p values and NSR1 gene

@@ Line 1: / Line 1: @@
 ==General Information and Metadata==
 *Strain analyzed: dASH1
-*Filename: DASH1 analysis QL.xlsx
+*Filename: DASH1_analysis QL.xlsx
 *Time points: 4
 **15 min

@@ Line 136: / Line 136: @@
 ==Summary Paragraph==
-In this experiment, the effect of cold shock on the expression of all of the genes in the dASH1 strain of yeast was measured. Data on collected at four separate time intervals (15 min, 30 min, 60 min, and 90 min). The first sixty minutes where under cold shock, while the last thirty were recovering from the cold shock. At each time interval, 4 measurements were taken at each time interval (except for 3 at 90 min) for a total of 15 measurements for each gene in the dASH1 yeast strain. In this week's assignment, the data from this experiment were analyzed. The average Log fold change at each time interval was analyzed for each gene, and different p values were calculated to determine the number of genes whose expression was affected by the cold shock. At an unadjusted  p-value of less than 0.05, 26.34% of the genes displayed changed expression in cold shock. At a more confident unadjusted p value of less than 0.01, 14.22% of the genes displayed changed expression in cold shock. At an even more confident unadjusted p value of 0.001, 5.75% of the genes displayed changed expression in cold shock. And at the highest unadjusted p value confidence of 0.0001, 2.29% of the genes displayed changed expression in cold shock. <br>
+In this experiment, the effect of cold shock on the expression of all of the genes in the dASH1 strain of yeast was measured. Data was collected at four separate time intervals (15 min, 30 min, 60 min, and 90 min). The first sixty minutes where under cold shock, while the last thirty were recovering from the cold shock. At each time interval, 4 measurements were taken (except for 3 at 90 min) for a total of 15 measurements for each gene in the dASH1 yeast strain. In this week's assignment, the data from this experiment were analyzed. The average Log fold change at each time interval was analyzed for each gene, and different p values were calculated to determine the number of genes whose expression was affected by the cold shock. At an unadjusted  p-value of less than 0.05, 26.34% of the genes displayed changed expression in cold shock. At a more confident unadjusted p value of less than 0.01, 14.22% of the genes displayed changed expression in cold shock. At an even more confident unadjusted p value of 0.001, 5.75% of the genes displayed changed expression in cold shock. And at the highest unadjusted p value confidence of 0.0001, 2.29% of the genes displayed changed expression in cold shock. <br>
 However, due to the high number of genes, a way to correct the multiple testing problem was needed. Thus the very strict Bonferroni-corrected p value and the slightly more lenient Benjamin and Hochberg-corrected p value were used to account for this. At a Bonferroni-corrected p value of less than 0.05, 0.856% of the genes displayed changed expression in cold shock. And at a Benjamin and Hochberg-corrected p value of less than 0.05, 11.80% of the genes displayed changed expression in cold shock. <br>
 Finally, the data on the gene NSR1 suggested that this gene was strongly affected by the cold shock, while my favorite gene, ADA2, was not affected by the cold shock (these findings are outlined in the section above).

@@ Line 1: / Line 1: @@
 ==General Information and Metadata==
 *Strain analyzed: dASH1
-*Filename: DASH1 analysis QL.zip
+*Filename: DASH1 analysis QL.xlsx
 *Time points: 4
 **15 min

@@ Line 146: / Line 146: @@
 ==Acknowledgements==
-*I worked in class with my homework partner [[User:Ebachour|Eddie Bachoura]] to assure that we were performing the correct data manipulations in excel. I also checked my final results with Eddie outside of class over text to ensure that we had arrived at the correct findings.
+*I worked in class with my homework partner [[User:Ebachour|Eddie Bachoura]] to assure that we were performing the correct data manipulations in excel. I also met with Eddie once outside of class to ensure that we had both performed the data anslysis correctly and that we had finished all of the deliverables.
 *I copied the template of the procedure from the [[Week_8|Week 8 assignment page]] to use as the template for my electronic journal. I modified this template to be specific for my particular strand dASH1.
 *[[User:Kdahlquist|Dr. Dahlquist]] for providing guidance on how to perform data analysis in Excel

@@ Line 148: / Line 148: @@
 *I worked in class with my homework partner [[User:Ebachour|Eddie Bachoura]] to assure that we were performing the correct data manipulations in excel. I also checked my final results with Eddie outside of class over text to ensure that we had arrived at the correct findings.
 *I copied the template of the procedure from the [[Week_8|Week 8 assignment page]] to use as the template for my electronic journal. I modified this template to be specific for my particular strand dASH1.
 *Microsoft Excel for providing the software with which to perform this data analysis. <br>
 [[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:40, 19 October 2017 (PDT)

@@ Line 136: / Line 136: @@
 ==Summary Paragraph==
-In this experiment, the effect of cold shock on the expression of all of the genes in the dASH1 strain of yeast was measured. Data on collected at four seperate time intervals (15 min, 30 min, 60 min, and 90 min). The first sixty minutes where under cold shock, while the last thirty were recovering from the cold shock. At each time interval, 4 measurements were taken at each time interval (except for 3 at 90 min) for a total of 15 measurements for each gene in the dASH1 yeast strain. In this week's assignment, the data from this experiment were analyzed. The average Log fold change at each time interval was analyzed for each gene, and different p values were calculated to determine the number of genes whose expression was affected by the cold shock. At an unadjusted  p-value of less than 0.05, 26.34% of the genes displayed changed expression in cold shock. At a more confident unadjusted p value of less than 0.01, 14.22% of the genes displayed changed expression in cold shock. At an even more confident unadjusted p value of 0.001, 5.75% of the genes displayed changed expression in cold shock. And at the highest unadjusted p value confidence of 0.0001, 2.29% of the genes displayed changed expression in cold shock. <br>
+In this experiment, the effect of cold shock on the expression of all of the genes in the dASH1 strain of yeast was measured. Data on collected at four separate time intervals (15 min, 30 min, 60 min, and 90 min). The first sixty minutes where under cold shock, while the last thirty were recovering from the cold shock. At each time interval, 4 measurements were taken at each time interval (except for 3 at 90 min) for a total of 15 measurements for each gene in the dASH1 yeast strain. In this week's assignment, the data from this experiment were analyzed. The average Log fold change at each time interval was analyzed for each gene, and different p values were calculated to determine the number of genes whose expression was affected by the cold shock. At an unadjusted  p-value of less than 0.05, 26.34% of the genes displayed changed expression in cold shock. At a more confident unadjusted p value of less than 0.01, 14.22% of the genes displayed changed expression in cold shock. At an even more confident unadjusted p value of 0.001, 5.75% of the genes displayed changed expression in cold shock. And at the highest unadjusted p value confidence of 0.0001, 2.29% of the genes displayed changed expression in cold shock. <br>
-However, due to the high number of genes, a way to correct the multiple testing problem was needed. Thus the very strict Bonferroni-corrected p value and the slightly more leanient Benjamin and Hochberg-corrected p value were used to account for this. At a Bonferroni-corrected p value of less than 0.05, 0.856% of the genes displayed changed expression in cold shock. And at a Benjamin and Hochberg-corrected p value of less than 0.05, 11.80% of the genes displayed changed expression in cold shock. <br>
+However, due to the high number of genes, a way to correct the multiple testing problem was needed. Thus the very strict Bonferroni-corrected p value and the slightly more lenient Benjamin and Hochberg-corrected p value were used to account for this. At a Bonferroni-corrected p value of less than 0.05, 0.856% of the genes displayed changed expression in cold shock. And at a Benjamin and Hochberg-corrected p value of less than 0.05, 11.80% of the genes displayed changed expression in cold shock. <br>
 Finally, the data on the gene NSR1 suggested that this gene was strongly affected by the cold shock, while my favorite gene, ADA2, was not affected by the cold shock (these findings are outlined in the section above).
 ==Deliverables==
-[[Media:DASH1 analysis QL.zip]]
+[[Media:DASH1 analysis QL.zip]] <br>
 [[Media:DASH1 Table QL.pptx]]

← Older revision		Revision as of 03:10, 20 October 2017
Line 12:		Line 12:

	number of timepoints = 4		number of timepoints = 4
		+
		+
		+	Unadjusted p value
		+	*Less than 0.05
		+	**1630
		+	**Percentage= 26.34%
		+	*Less than 0.01
		+	**880
		+	**Percentage= 14.22%
		+	*Less than 0.001
		+	**356
		+	**Percentage= 5.75%
		+	*Less than 0.0001
		+	**142
		+	**Percentage= 2.29%
		+
		+	Bonferroni-corrected p value
		+	*Less than 0.05
		+	**53
		+	**Percentage= 0.856%
		+
		+	Benjamin and Hochberg-corrected p value
		+	*Less than 0.05
		+	**730
		+	**Percentage= 11.80%
		+
		+	NSR1 gene
		+	*p values
		+	**unadjusted: 2.92024E-06
		+	**Bonferroni-corrected: 0.018073394
		+	**Benjamin and Hochberg-corrected: 0.000430319
		+	*Average Log fold changes
		+	**At 15 min: 1.886696138
		+	**At 30 min: 2.611946831
		+	**At 60 min: 1.394879511
		+	**At 90 min: -2.673801047
		+
		+	The NSR1 gene most certainly changes expression due to the cold shock in this experiment. This is apparent from the large values for all of the Log fold changes at every time interval (as a 0 Log value would mean no change in expression and thus a large non-zero Log value means a large change in expression).
		+


	[[Media:DASH1 analysis QL.zip]]		[[Media:DASH1 analysis QL.zip]]