updated 2.3 years ago by
shijieczheng
•
0
•
written 2.3 years ago by
bony.dekumar
▴
10
0
votes
2
replies
811
views
Recent ...
Replies
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…
Answer: edgeR::cpm() results in negative values from raw counts of 0
by
ATpoint
★
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=…
Votes
Awards
• All
Popular Question to
Gordon Smyth
52k
Popular Question to
shepherl
4.1k
Popular Question to
Mengjun
•
0
Popular Question to
Dario Strbenac
★
1.6k
Locations
• All
United States, 3 minutes ago
United Kingdom, 18 minutes ago
Finland, 36 minutes ago
Australia/Melbourne/Monash University Genomics and Bioinformatics Platform, 50 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
United States, 3 minutes ago
United Kingdom, 18 minutes ago
Finland, 36 minutes ago
Australia/Melbourne/Monash University Genomics and Bioinformatics Platform, 50 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Traffic: 856 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6