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Eugene Bolotin
▴
20
@eugene-bolotin-6300
Last seen 10.2 years ago
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