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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=…
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Leonardo Collado Torres
★
1.1k
Thanks for posting this Kinnary. See also https://github.com/LieberInstitute/spatialLIBD/issues/106 for more details on the background.
Answer: Gene Ontology (GO) Analysis
by
James W. MacDonald
68k
The main difference is that `enrichGO` fits a conventional hypergeometric test whereas `hyperGTest` allows you to do a conditional test as …
Comment: blockwiseModule crashes in the end and doesn't generate modules
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drivingdirectionsonline
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0
Solution: The error is likely due to a conflicting cor() function from another package (like psych). Restart R, run blockwiseModules() befo…
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