[Bioc-devel] Possible bug in edgeR::aveLogCPM.default?

Ryan C. Thompson rct at thompsonclan.org
Fri Jul 11 23:25:56 CEST 2014


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?


-Ryan Thompson

More information about the Bioc-devel mailing list