Hi,

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.

Priyanka 

Most likely someone upgraded the package versions. Either way, just use the ‘contrast’ argument to extract the specific contrasts you need.