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written 2.2 years ago by
Wolfgang Huber
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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…
Answer: edgeR::cpm() results in negative values from raw counts of 0
by
James W. MacDonald
68k
It's calculated exactly how you might expect (it's called counts/million counts for a reason).
```
> y <- matrix(rnbinom(20,size=1,mu=…
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Leonardo Collado Torres
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1.1k
Thanks for posting this Kinnary. See also https://github.com/LieberInstitute/spatialLIBD/issues/106 for more details on the background.
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