[BioC] Incorrect result in edgeR.calculateCommonDispersion

[Gordon K Smyth]

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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