[BioC] Incorrect result in edgeR.calculateCommonDispersion

Jacob Silterra jacob at broadinstitute.org
Wed Jun 4 19:45:50 CEST 2014

Hello all,

I've encountered an issue with edgeR when it calculates dispersion, and
there aren't any samples for a given group. I believe it happens with both
tagwise and common dispersion; same idea. Basically splitIntoGroups will
return an empty matrix for that group, which messes up the dispersion
calculation. I think it would be better to ignore groups that have no data
associated with them. Example attached. This might seem unnecessary, but I
have a situation where I read in a matrix with samples of different classes
and then remove some groups entirely

Jacob Silterra
Associate Computational Biologist
Broad Institute

More information about the Bioconductor mailing list