[BioC] DESeq2 design formula error?

[Steve Lianoglou]

Hi Charles,


On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr <deter088 at umn.edu> wrote:
> Greetings,
>
> I am trying to run an interaction formula with DESeq2.  I try and run the
> following code and get the following error:
>
>> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds <- DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had estimated dispersions, replacing thesegene-wise dispersion estimatesError in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- convertNames$to :
>   NAs are not allowed in subscripted assignments
>
>
> I am not sure exactly what this means.  I have uneven groups sizes but it
> doesn't seem to be an issue when I have the design:
>
>> design(DESeq.cds) <- formula(~ subject+times+group+group:times)
>
>
> But the above formula doesn't provide the contrasts I would like.  I would
> like to have the coefficients to be as follows so I can report how the
> genes change in response in the different groups over time.

This is related to my recent posting over @ bioc-devel which Mike just
committed a fix for:

https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004463.html

The good news is that Mike has patched the current and devel versions,
so you should be able to get them soon once version 1.0.18 propagates
through the build system:

https://stat.ethz.ch/pipermail/bioc-devel/2013-July/004503.html

Or, optionally, you can d/l from SVN and compile/install yourself, if
you are equipped to do so.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech