Dear all, I am using DESeq package to analyze differences of expression of miRNA from short sequence data. I have a subset of sequences for which I am analyzing differences between treatment NS vs treatment S the code I am using is conds_celltype<-c("NS","NS","NS","S","S","S","S","S","S") cds_pi_ct<-newCountDataSet(countsTable_pi,conds_celltype) cds_pi_ct<-estimateSizeFactors(cds_pi_ct) sizeFactors(cds_pi_ct) cds_pi_ct<-estimateVarianceFunctions(cds_pi_ct) res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S") resSig_pi_ct<-res_pi_ct[res_pi_ct$padj<.1,] resSig_pi_ct but I am getting an error message when I am making the test, res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S") Error: is.finite(pobs) is not TRUE In addition: Warning message: In dnbinom(x, size, prob, log) : NaNs produced I don't understand this, I have used this code for another subset of sequences and it worked just fine. Can someone tell me what I am doing wrong? Thanks Andreia Session Info: sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 [4] LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] DESeq_0.7.12 locfit_1.5-6 lattice_0.17-26 akima_0.5-4 Biobase_2.6.1 loaded via a namespace (and not attached): [1] annotate_1.24.1 AnnotationDbi_1.8.2 DBI_0.2-5 genefilter_1.28.2 geneplotter_1.24.0 grid_2.10.1 [7] RColorBrewer_1.0-2 RSQLite_0.8-4 splines_2.10.1 survival_2.35-7 xtable_1.5-6 -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]

Dear Andreia Thank you for the feedback! The first thing to do here is to use a more recent version of DESeq (last release was 1.0.4, the current devel is 1.1.5). If that fails, the second is to make available (e.g. by using the "dump" function in R or by posting the saved "countsTable_pi" object on a http-server) the offending data so that we can reproduce your problem. Best wishes Wolfgang On Jun/21/10 6:48 PM, Andreia Fonseca wrote: > Dear all, > > I am using DESeq package to analyze differences of expression of miRNA from > short sequence data. > I have a subset of sequences for which I am analyzing differences between > treatment NS vs treatment S > the code I am using is > conds_celltype<-c("NS","NS","NS","S","S","S","S","S","S") > cds_pi_ct<-newCountDataSet(countsTable_pi,conds_celltype) > cds_pi_ct<-estimateSizeFactors(cds_pi_ct) > sizeFactors(cds_pi_ct) > cds_pi_ct<-estimateVarianceFunctions(cds_pi_ct) > res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S") > resSig_pi_ct<-res_pi_ct[res_pi_ct$padj<.1,] > resSig_pi_ct > > but I am getting an error message when I am making the test, > > res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S") > Error: is.finite(pobs) is not TRUE > In addition: Warning message: > In dnbinom(x, size, prob, log) : NaNs produced > > > I don't understand this, I have used this code for another subset of > sequences and it worked just fine. Can someone tell me what I am doing > wrong? > Thanks > Andreia > > Session Info: > > sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=Portuguese_Portugal.1252 > LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252 > [4] LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252 > > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] DESeq_0.7.12 locfit_1.5-6 lattice_0.17-26 akima_0.5-4 > Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] annotate_1.24.1 AnnotationDbi_1.8.2 DBI_0.2-5 > genefilter_1.28.2 geneplotter_1.24.0 grid_2.10.1 > [7] RColorBrewer_1.0-2 RSQLite_0.8-4 splines_2.10.1 > survival_2.35-7 xtable_1.5-6 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber