Hi Charles,

On Tuesday, July 16, 2013, Charles Determan Jr wrote:

> Thank you Steve and to Mike as well for the patch.  Do you (or anyone) if
> there is a rough timeline as to when the patched package will be made
> available?  I am on a restricted timeline and I have not compiled and
> installed an R package before but I will certainly give it a try if the
> patched package won't be out soon.


I'm actually surprised that it hasn't propagated over to the servers yet
... perhaps it will be there later today (noon-ish PST) or tomorrow

Compiling and installing yourself is as easy as running "R CMD INSTALL
package_name" (depending on the os you are on) so I'd definitely recommend
you try that.

You need to ensure you have a valid build tool gain on your machine that
includes gcc. If you are running osx or Linux, setting up a sane build
environment is quite easy. From what I understand, it is also relatively
easier to set this up on windows with newer versions of r (you should be on
3.0.x anyway) ... So, I think you can give it a shot to see?

-Steve


> Thanks again,
> Charles
>
>
> On Mon, Jul 15, 2013 at 3:45 PM, Steve Lianoglou
> <lianoglou.steve@gene.com <javascript:;>>wrote:
>
> > Hi Charles,
> >
> >
> > On Mon, Jul 15, 2013 at 12:23 PM, Charles Determan Jr <deter088@umn.edu<javascript:;>
> >
> > 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
> >
>
>
>
> --
> Charles Determan
> Integrated Biosciences PhD Candidate
> University of Minnesota
>
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>
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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech

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