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
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
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
