updated 7.5 years ago by
Gordon Smyth
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written 7.5 years ago by
Pekka Kohonen
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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
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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…
Answer: edgeR::cpm() results in negative values from raw counts of 0
by
ATpoint
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4.8k
The function, when `log = TRUE` adds a small prior count to the counts before taking the log, avoiding taking the log of 0. If that prior i…
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