Matthew E. Jurek Week 9

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.
7. 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
8. 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
9. 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
10. 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