Kevin Matthew McKay Week 9

assignment Kevin McKay

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

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

• 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