# Kevin Matthew McKay Week 9

(Difference between revisions)
 Revision as of 14:10, 2 April 2013 (view source) (4 questions)← Previous diff Current revision (15:06, 2 April 2013) (view source) (questions) (6 intermediate revisions not shown.) Line 2: Line 2: [[User:Kevin Matthew McKay|Kevin McKay]] [[User:Kevin Matthew McKay|Kevin McKay]] [[Category:BIOL398-03/S13]] [[Category:BIOL398-03/S13]] + + ==Pval== *t15 *t15 **1474 genes have p value < 0.05 **1474 genes have p value < 0.05 Line 27: Line 29: **9 genes have p < 0.001 **9 genes have p < 0.001 **1 gene have p < 0.0001 **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 + ==NSR1== + *avg + **t15:2.04 + **t30:2.21 + **t60:2.43 + **t90:-1.59 + **t120:-.056 + + *pval + **t15:.0174 + **t30:.0320 + **t60:.0020 + **t90:.0102 + **t120:.2257 + + ==more questions 2== + *Smallest pval is 0.0000454949980265369 for gene YJR100C + *Gene function is unknown, maybe the function of this gene has something to do with adaptation or acclimation to cold

## 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
• pval
• t15:.0174
• t30:.0320
• t60:.0020
• t90:.0102
• t120:.2257

## more questions 2

• Smallest pval is 0.0000454949980265369 for gene YJR100C
• Gene function is unknown, maybe the function of this gene has something to do with adaptation or acclimation to cold