Sure, here it is : R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.2.10 RcppArmadillo_0.4.100.2.1 Rcpp_0.11.0 GenomicRanges_1.14.4 XVector_0.2.0 [6] IRanges_1.20.7 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 lattice_0.20-27 [8] locfit_1.5-9.1 RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-7 XML_3.98-1.1 [15] xtable_1.7-3 Hugo Hugo Varet Plate-Forme Transcriptome et Epigénome Institut Pasteur Mél. : hugo.varet@pasteur.fr Tél. : 01-40-61-35-13 Le 11/03/2014 15:50, Michael Love a écrit : > > Hi Hugo, > > Can you provide the ouput of sessionInfo() > > Mike > > On Mar 11, 2014 10:38 AM, "Hugo Varet" > wrote: > > Dear Mike Love and list members, > > I'm running DESeq2 with a design containing two covariates: the > first is dichotomous while the second is continuous. Here is the > data.frame I put in colData(dds): > sample dicho conti > 1 0 4.577032 > 2 0 4.462997 > 3 1 5.024896 > 4 1 4.543696 > 5 1 5.542576 > 6 1 5.356217 > 7 1 4.593729 > 8 1 4.243286 > 9 1 5.164055 > 10 0 4.565966 > 11 0 4.565966 > 12 0 4.760724 > 13 1 5.428459 > 14 1 4.515874 > 15 1 4.412964 > 16 1 4.426836 > > I chose to study the design (~ dicho + conti) and to test the > effect of the continuous covariate on the counts (about 15,000 > features). I can compute the size factors, but when estimating the > dispersions, I get the following error: > > dds <- estimateDispersions(dds) > gene-wise dispersion estimates > error: inv(): matrix appears to be singular > Erreur : inv(): matrix appears to be singular > > I think the error does not come from the design which is of full > rank and which works if I use a subset of the features. Moreover, > with a design as (~ dicho + conti + dicho:conti), I do not meet > the error ! Do you have any idea of the origin of the problem ? > > Best regards, > > Hugo > > -- > Hugo Varet > Plate-Forme Transcriptome et Epigénome > Institut Pasteur > Mél. : hugo.varet@pasteur.fr > Tél. : 01-40-61-35-13 > > _______________________________________________ > 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 > [[alternative HTML version deleted]]