# Kevin Matthew McKay Week 9

(Difference between revisions)
 Revision as of 13:39, 2 April 2013 (view source) (numbers)← Previous diff Revision as of 13:40, 2 April 2013 (view source) (title)Next diff → Line 33: Line 33: *t15-t90 0 genes have p < 0.05 *t15-t90 0 genes have p < 0.05 *t120 1 gene has 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? *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 **613

## 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