Hello, I'm struggling with batch correction for RNA-seq data in DESeq2. For example, my colData looks like this (10 samples, 6 controls+4 treatment, belong to 2 batches):
samples condition batch 100 PH7 1 101 PH7 1 103 PH7 1 63 PH7 1 64 ctr 1 74 ctr 1 75 ctr 1 76 ctr 2 88 ctr 2 99 ctr 2
As far as I understood from this post, my problem is that some conditions belongs only to one batch, for example, all "PH7" belong only to 1 batch. I tried to do as was suggested on the post:
mm = model.matrix(~ batch+conditions, colData(dds))
And then look up for columns where ALL zeros, however, I don't have such... At least in one raw of each column there is 1.
Is there a way to make such analysis?