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

14 January 2016

Genewise expression level

Spreadsheet, voom plot

2360 with fdr<=0.01

3386 with fdr<=0.05



Raw data format: Sample_E1_Ca1; Sample_E1_Ca6; Sample_E1_Ca9; Sample_E3_Ca1; Sample_E3_Ca6; Sample_E3_Ca9
5757 of 6214 features kept after filtering
(required at least one sample with 10 reads)
df = 7.988469
sd = 1.091117
noise combined p-value = 0.098012
noise fit score = 0.223237 bits

Design matrix

[--------------] test coefficients
      0       0       1       0  Sample_E1_Ca1
      1       0       1       0  Sample_E1_Ca6
      0       1       1       0  Sample_E1_Ca9
      0       0       1       1  Sample_E3_Ca1
      1       0       1       1  Sample_E3_Ca6
      0       1       1       1  Sample_E3_Ca9