Differential expression with Mac T1 as baseline vs T6, T9, with the batch effect accounted for and removed.

14 January 2016

Genewise expression level

Spreadsheet, voom plot

72 with fdr<=0.01

222 with fdr<=0.05



Raw data format: Sample_E1_Mac1; Sample_E1_Mac6; Sample_E1_Mac9; Sample_E3_Mac1; Sample_E3_Mac6; Sample_E3_Mac9
12766 of 45084 features kept after filtering
(required at least one sample with 10 reads)
df = 18.137394
sd = 1.085830
noise combined p-value = 0.181808
noise fit score = 0.454050 bits

Design matrix

[--------------] test coefficients
      0       0       1       0  Sample_E1_Mac1
      1       0       1       0  Sample_E1_Mac6
      0       1       1       0  Sample_E1_Mac9
      0       0       1       1  Sample_E3_Mac1
      1       0       1       1  Sample_E3_Mac6
      0       1       1       1  Sample_E3_Mac9