Is 100K genes too many to run ComBat_seq on?
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zeegzaag • 0
@user-24987
Last seen 2.2 years ago
United Kingdom

Hello,

I am trying to run sva::ComBat_seq on some count data, i have 100K genes, it doesn't seem to finish running, does ComBat have a limit? Should I reduce the number of genes I am working with?

Thanks in advance.

RNASeqRData combat_Seq BatchEffect • 842 views
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Hi,

When you say you have 100,000 genes do you mean you have counts of transcripts? With all the genes, pseudogenes and other elements my typical counts matrix is about 56K.

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Hello, Yes, 100K transcripts. I have been trying to run this for almost a day now and it doesn't seem to be running...

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