[Bioc-devel] renameModelMatrixColumns mishap + patch for DESeq2

[Steve Lianoglou]

Hey Mike,

On Tue, Jul 9, 2013 at 11:52 PM, Michael Love
<michaelisaiahlove at gmail.com> wrote:
> Hi Steve,
>
> Thanks for pointing out this bug in the renaming code. I will fix this as
> soon as possible.

If you decide to go the `subset(convertNames, ...)` route that I suggested:

(1) You might want to put this in the renameModelMatrixColumns itself
instead of where I suggested; and

(2) be sure to guard the `subset` against the case when
renameModelMatrixColumns return a 0 row data.frame, which is the case
when you set design(dds) <- ~ 1. I just got bit by this when I was
using the default params of the various variance stabilizing
transforms.

Anyway, I'm sure you'll find a better way to handle this stuff, but
just wanted to give you advanced warning.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech