Hello,
I think I may have found a bug in the code for aveLogCPM.default in the
edgeR package. Near the end of the function, the variable
"prior.count.scale" is conditionally assigned to, and never subsequently
used. I assume this is a typo and the variable name is supposed to be
"prior.count.scaled" instead. Thus, this code is essentially a no-op.
I'm not sure what the implications of skipping this line are or when
this code would be executed. The line in question is this:
if(is.null(dim(prior.count.scaled))) prior.count.scale <-
matrix(1,nrow(y),1) %*% prior.count.scaled
I downloaded the current development tarball from the Bioconductor site,
and this also seems to have the same issue.
On a side, note, the edgeR page lists 4 maintainers. Which one is the
best one to email about bug reports, or should I cc all of them?
Thanks,
-Ryan Thompson
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