I am trying to account for batch effect in the DESeq2 design as follows:
ddsFull<-DESeqDataSetFromMatrix(countData=countsTable, colData=colData, design=~batch+group)
My covariate of interest is "group" and has three levels 1A, 1B, 2A. I have 2 batches - A and B that need to be accounted for.
However, when I run dds<-DESeq(ddsFull) and check resultsNames(dds) it gives me: "Intercept" "batch_B_vs_A" "group1B_vs_1A" "group2A_vs_1A"
A few days back when I ran the code it allowed me to correct for batch and let me extract results for the three contrasts comparing the three group (1B_vs1A, 2A_vs_1A, 2A_vs_1B). I don't understand what has changed between last time and now.
Appreciate any help.