Got 15 samples, and got: 16 data fields. Header: cold_01 warm_01 cold_02 warm_02 cold_03 cold_04 cold_05 warm_03 warm_04 warm_05 cold_06 cold_07 cold_08 warm_06 cold_09 Next: TRINITY_DN0_c0_g1 1.87 311.17 1307.97 5342.69 0.00 0.00 0.00 0.00 0.00 3.39 0.00 0.00 0.00 1.91 1.50 $VAR1 = { 'warm_01' => 2, 'cold_08' => 13, 'cold_02' => 3, 'warm_05' => 10, 'cold_07' => 12, 'cold_04' => 6, 'cold_03' => 5, 'cold_06' => 11, 'cold_01' => 1, 'cold_05' => 7, 'cold_09' => 15, 'warm_06' => 14, 'warm_03' => 8, 'warm_02' => 4, 'warm_04' => 9 }; Contrasts to perform are: $VAR1 = [ [ 'cold', 'warm' ] ]; Loading required package: edgeR Loading required package: limma