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

12 January 2016

Genewise expression level

Spreadsheet, voom plot

739 with fdr<=0.01

1414 with fdr<=0.05



Raw data format: Sample_E1_CaMac1; Sample_E1_CaMac6; Sample_E1_CaMac9; Sample_E3_CaMac1; Sample_E3_CaMac6; Sample_E3_CaMac9
5651 of 6214 features kept after filtering
(required at least one sample with 10 reads)
df = 12.270798
sd = 1.032459
noise combined p-value = 0.001322
noise fit score = 0.671477 bits

Design matrix

[--------------] test coefficients
      0       0       1       0  Sample_E1_CaMac1
      1       0       1       0  Sample_E1_CaMac6
      0       1       1       0  Sample_E1_CaMac9
      0       0       1       1  Sample_E3_CaMac1
      1       0       1       1  Sample_E3_CaMac6
      0       1       1       1  Sample_E3_CaMac9