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]]