I am running an RNA Seq analysis for differential gene expressions for the following Biological Replicates: 3 Control, 3 Treatment A, 3 Treatment B, and 3 Treatment C.
I need to make the following comparisons: Treatment A vs Treatment B vs Treatment C with control as the reference. I am confused as to how should I write the contrasts.
This is how I have been doing it: exp_res <- results(dds, contrast = list( c("condition4HT-treated", "conditionENDX-treated"), c("condition4HT-treated", "conditionICI-treated"), c("conditionENDX-treated", "conditionICI-treated") ), alpha = 0.05, lfcThreshold = 0)
However, I am facing this error: Error in checkContrast(contrast, resNames) : 'contrast', as a list, should have length 2, or, if length 1, an empty vector will be added for the second element.
Thank you for your help.