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Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k
Thanks for the answer James! I had forgotten about the "PM" part of CPM when I met with Kinnary yesterday!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k
Thank you Gordon for the detailed answer, examples, and link to the unpublished thesis!
Answer: Make DEXSeq plot normal scale by James W. MacDonald 68k
It's hard coded, so you will not be able to change the vertical axis of the top plot without getting the code and modifying. You can simply…
Answer: RNA Seq using Lrt by James W. MacDonald 68k
When you perform an LRT, you are testing the coefficients that are no longer included in the reduced model. So you are testing to see if in…
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Gordon Smyth 52k
Mmm, I am not at all attracted to those approaches. Perhaps the use of `log(cpm+1)` might facilitate the use of sparse methods in other pac…
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Comment: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
edgeR::cpm() results in negative values from raw counts of 0
Answer: edgeR::cpm() results in negative values from raw counts of 0
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