[Bioc-devel] Bug in voom/cbind for EList

Gordon K Smyth smyth at wehi.EDU.AU
Wed Jun 5 02:40:40 CEST 2013

Hi Ryan,

Thanks for the heads-up.  lib.size and design weren't originally intended 
to be core components of an EList object, hence they weren't recognized in 
the subsetting and cbinding.

Anyway, I have now committed a fix to limma on bioc-devel so that lib.size 
and design are now respected by subsetting and cbinding.  voom() now 
stores the (effective) lib.size as a column of the targets data.frame 
rather than as a separate component.

Best wishes

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.

On Tue, 4 Jun 2013, Ryan C. Thompson wrote:

> Hi Gordon,
> I'm implementing the "voom-by-group" procedure that you suggested previously, 
> and I'm running into a small snag: when I call voom several times to get 
> several EList objects, I then need to cbind them together. However, the 
> design and lib.size components of the ELists are not merged, but rather are 
> simply taken from the first element. Also, when subsetting an EList by 
> columns, it seems that lid.size does not get subsetted, but is copied whole.
> Obviously I can work around these issues after having discovered them, but I 
> wanted to let you know in case you want to fix them.
> -Ryan

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