# Kevin Matthew McKay Week 9

(Difference between revisions)
 Revision as of 14:40, 2 April 2013 (view source) (title)← Previous diff Revision as of 14:50, 2 April 2013 (view source) (nsr1)Next diff → Line 42: Line 42: *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.) **815 **815 + ==NSR1== + *avg + **t15:2.04 + **t30:2.21 + **t60:2.43 + **t90:-1.59 + **t120:-.056

## Pval

• t15
• 1474 genes have p value < 0.05
• 345 genes have p < 0.01
• 30 genes have p < 0.001
• 4 genes have p < 0.0001
• t30
• 946 genes have p value < 0.05
• 266 genes have p < 0.01
• 34 genes have p < 0.001
• 6 genes have p < 0.0001
• t60
• 1006 genes have p value < 0.05
• 274 genes have p < 0.01
• 35 genes have p < 0.001
• 0 genes have p < 0.0001
• t90
• 732 genes have p value < 0.05
• 190 genes have p < 0.01
• 12 genes have p < 0.001
• 1 gene have p < 0.0001
• t120
• 397 genes have p value < 0.05
• 89 genes have p < 0.01
• 9 genes have p < 0.001
• 1 gene have p < 0.0001

## After Bonferi Correction

• t15-t90 0 genes have p < 0.05
• t120 1 gene has p < 0.05

## more questions

• 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?
• 613
• 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?
• 861
• Keeping the "Pval" filter at p < 0.05, How many have an average log fold change of >0.25 and p < 0.05?
• 600
• 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.)
• 815

• avg
• t15:2.04
• t30:2.21
• t60:2.43
• t90:-1.59
• t120:-.056