Dear all, I???m trying to use DESeq2 but I get this error message when I try the code: res <- results(dds) Error in is.numeric(cooksCutoff) : 'cooksCutoff' is missing I can't find any answer about this error. Could you please help me? Thanks in advance! Cheers Natalia -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 easyRNASeq_1.8.3 ShortRead_1.20.0 Rsamtools_1.14.2 [7] GenomicRanges_1.14.3 DESeq_1.14.0 lattice_0.20-24 locfit_1.5-9.1 Biostrings_2.30.1 XVector_0.2.0 [13] IRanges_1.20.6 edgeR_3.4.1 limma_3.18.3 biomaRt_2.18.0 Biobase_2.22.0 genomeIntervals_1.18.0 [19] BiocGenerics_0.8.0 intervals_0.14.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-6 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 [8] hwriter_1.3 latticeExtra_0.6-26 LSD_2.5 RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.2 [15] stats4_3.0.2 survival_2.37-4 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.

hi Natalia, Sorry about this. It is a simple bug for when number of samples = number of coefficients to fit. I am pushing out a fix now (v1.2.7) which will be available in ~1 day, and I will add a unit test for such designs to devel. Mike On Wed, Dec 4, 2013 at 3:56 AM, Natalia [guest] <guest@bioconductor.org>wrote: > > Dear all, > I’m trying to use DESeq2 but I get this error message when I try the code: > res <- results(dds) > Error in is.numeric(cooksCutoff) : 'cooksCutoff' is missing > > I can't find any answer about this error. Could you please help me? > Thanks in advance! > > Cheers > > Natalia > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] DESeq2_1.2.6 RcppArmadillo_0.3.920.3 Rcpp_0.10.6 > easyRNASeq_1.8.3 ShortRead_1.20.0 Rsamtools_1.14.2 > [7] GenomicRanges_1.14.3 DESeq_1.14.0 lattice_0.20-24 > locfit_1.5-9.1 Biostrings_2.30.1 XVector_0.2.0 > [13] IRanges_1.20.6 edgeR_3.4.1 limma_3.18.3 > biomaRt_2.18.0 Biobase_2.22.0 genomeIntervals_1.18.0 > [19] BiocGenerics_0.8.0 intervals_0.14.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationDbi_1.24.0 bitops_1.0-6 > DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.2 > [8] hwriter_1.3 latticeExtra_0.6-26 LSD_2.5 > RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 > splines_3.0.2 > [15] stats4_3.0.2 survival_2.37-4 XML_3.98-1.1 > xtable_1.7-1 zlibbioc_1.8.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]