Hi all, it has, this morning. I have installed other package and it has
asked me to updated it.

J
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
*[1] DESeq2_1.0.18      *     RcppArmadillo_0.3.900.0 Rcpp_0.10.4

[4] lattice_0.20-15         Biobase_2.20.1          GenomicRanges_1.12.4
[7] IRanges_1.18.2          BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.22.6 DBI_0.2-7            RColorBrewer_1.0-5
 [4] RSQLite_0.11.4       XML_3.95-0.2         annotate_1.38.0
 [7] genefilter_1.42.0    grid_3.0.1           locfit_1.5-9.1
[10] splines_3.0.1        stats4_3.0.1         survival_2.37-4
[13] tools_3.0.1          xtable_1.7-1



2013/7/16 Steve Lianoglou <lianoglou.steve@gene.com>

> 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
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org <javascript:;>
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Jose M. Garcia Manteiga PhD
Research Assistant - Data Analysis in Functional Genomics
Center for Translational Genomics and BioInformatics
Dibit2-Basilica, 3A3
San Raffaele Scientific Institute
Via Olgettina 58, 20132 Milano (MI), Italy

Tel: +39-02-2643-4751
e-mail: garciamanteiga.josemanuel@hsr.it

	[[alternative HTML version deleted]]

