[BioC] EdgeR Design matrix not of full rank. The following coefficients not estimable errorR

Eugene Bolotin elbolotin at gmail.com
Sun Dec 22 06:30:33 CET 2013

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,

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