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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…
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Paul Harrison
▴
100
One purely practical advantage to keeping zeros zero in particular is that sparse matrices stay sparse (using the `log1p` function). I thin…
Answer: edgeR::cpm() results in negative values from raw counts of 0
by
Gordon Smyth
52k
**logCPM values decrease as the library size increases**
`edgeR::cpm` computes logCPM values according to the formula `log2( (y + y0) / (L…
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Gordon Smyth
52k
Thanks answering this question. Let me say though that I've never understood why people would find negative log values to be annoying or un…
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