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

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
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth

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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