[BioC] Incorrect result in edgeR.calculateCommonDispersion
Gordon K Smyth
smyth at wehi.EDU.AU
Thu Jun 5 02:21:28 CEST 2014
Dear Jacob,
There is no function called edgeR.calculateCommonDispersion in the edgeR
package.
There also wasn't any attachment with your posting.
If you subset a DGEList in such a way that a group is removed entirely,
you can prevent any problems by resetting the levels of the group factor:
dge$samples$group <- factor(dge$samples$group)
Best wishes
Gordon
----------- original message ------------
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
Thanks,
--
Jacob Silterra
Associate Computational Biologist
Broad Institute
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