# Matthew E. Jurek Week 9

(Difference between revisions)
 Revision as of 21:59, 2 April 2013 (view source) (→Sanity Check: deleted timepoints except for t30)← Previous diff Revision as of 22:10, 2 April 2013 (view source) (→Sanity Check: corrected last 4 questions)Next diff → Line 30: Line 30: ##t90= 0 ##t90= 0 ##t120= 0 ##t120= 0 - For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following: + #For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following: - #Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? + Following the correction, there were no p values <.05.  Thus, the following are calculations for each time point + Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria? + ##t15= 203 ##t30= 332 ##t30= 332 + ##t60= 168 + ##t90= 118 + ##t120= 104 #Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? #Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria? + ##t15= 182 ##t30= 212 ##t30= 212 + ##t60= 266 + ##t90= 86 + ##t120= 86 #Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? #Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05? + ##t15= 0 ##t30= 0 ##t30= 0 + ##t60= 0 + ##t90= 0 + ##t120= 0 #How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.) #How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.) + ##t15= 150 ##t30= 198 ##t30= 198 + ##t60= 247 + ##t90= 63 + ##t120= 74

## Sanity Check

1. How many genes have p value < 0.05?
1. t15= 385
2. t30= 544
3. t60= 434
4. t90= 231
5. t120= 190
2. What about p < 0.01?
1. t15= 81
2. t30= 108
3. t60= 87
4. t90= 28
5. t120= 34
3. What about p < 0.001?
1. t15= 8
2. t30= 10
3. t60= 6
4. t90= 5
5. t120= 4
4. What about p < 0.0001?
1. t15= 0
2. t30= 1
3. t60= 1
4. t90= 1
5. t120= 0
5. Perform this correction and determine whether and how many of the genes are still significantly changed at p < 0.05 after the Bonferroni correction.
1. t15= 0
2. t30= 0
3. t60= 0
4. t90= 0
5. t120= 0
6. For the timepoint that had the greatest number of genes significantly changed at p < 0.05, answer the following:

Following the correction, there were no p values <.05. Thus, the following are calculations for each time point Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change greater than zero. How many meet these two criteria?

1. t15= 203
2. t30= 332
3. t60= 168
4. t90= 118
5. t120= 104
1. Keeping the "Pval" filter at p < 0.05, filter the "AvgLogFC" column to show all genes with an average log fold change less than zero. How many meet these two criteria?
1. t15= 182
2. t30= 212
3. t60= 266
4. t90= 86
5. t120= 86
2. Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of > 0.25 and p < 0.05?
1. t15= 0
2. t30= 0
3. t60= 0
4. t90= 0
5. t120= 0
3. How many have an average log fold change of < -0.25 and p < 0.05? (These are more realistic values for the fold change cut-offs because it represents about a 20% fold change which is about the level of detection of this technology.)
1. t15= 150
2. t30= 198
3. t60= 247
4. t90= 63
5. t120= 74