Kevin Matthew McKay Week 9

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assignment Kevin McKay

Contents

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

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
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