Dear Gordon, I apologize if I was a bit unclear, I actually simplified my problem a little bit so it would fit into this bio-conductor post. I actually have 10+ samples in batch 1157, but that batch does not contain any "tumor" samples. I have additional similar batches some with tumor "some" without "tumor" samples. I want to remove batch specific differences between all samples. edgeR however gives me the same error, no matter how many samples I have in the batch, but does not give me this error if I remove all batches which do not contain any "tumor" samples. Can I just take residuals of logged count data after performing the linear regression on the batch factor? Can I then then feed the residuals into edgeR linear modeling? I want to compare how much each sample/patient/vector differs from average "tumor" sample. The batches are quite large with >10 samples each, and I have ~300 total samples. Thanks a ton, Eugene