Got 18 samples, and got: 19 data fields. Header: cold_01 ambient_01 ambient_02 cold_02 ambient_03 cold_03 cold_04 cold_05 ambient_04 ambient_05 ambient_06 cold_06 cold_07 cold_08 ambient_07 ambient_08 ambient_09 cold_09 Next: TRINITY_DN0_c0_g1 1.87 2.00 1749.29 1307.89 1991.04 0.00 0.00 0.00 1.89 2.47 0.00 0.00 0.00 0.00 2.62 0.00 6.13 1.50 $VAR1 = { 'ambient_09' => 17, 'cold_02' => 4, 'ambient_04' => 9, 'ambient_06' => 11, 'cold_03' => 6, 'ambient_01' => 2, 'cold_06' => 12, 'ambient_08' => 16, 'ambient_02' => 3, 'cold_09' => 18, 'ambient_03' => 5, 'cold_08' => 14, 'ambient_07' => 15, 'cold_07' => 13, 'cold_04' => 7, 'ambient_05' => 10, 'cold_01' => 1, 'cold_05' => 8 }; Contrasts to perform are: $VAR1 = [ [ 'ambient', 'cold' ] ]; Loading required package: edgeR Loading required package: limma