Dear Wolfgang, just to say no error with last version of the package. kind regards, Andreia On Thu, Jul 8, 2010 at 11:15 PM, Andreia Fonseca <andreia.fonseca@gmail.com>wrote: > Dear Wolfgang, > > please disregard my last email, it was missing package xtable, DESeq is > loaded now. > with kind regards > Andreia > > > On Thu, Jul 8, 2010 at 10:44 PM, Andreia Fonseca < > andreia.fonseca@gmail.com> wrote: > >> Dear Wolfgang, >> >> I am using a windows machine and I just have installed R 2.11.1 and I am >> trying to install the last version of DESeq. The installation seems ok but I >> am getting an error while uploading the library: >> >> library(DESeq) >> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : >> there is no package called 'xtable' >> Error: package/namespace load failed for 'DESeq' >> >> maybe there is a bug? >> >> thanks for the help >> kind regards, >> Andreia >> >> >> On Tue, Jun 29, 2010 at 4:57 PM, Wolfgang Huber <whuber@embl.de> wrote: >> >>> 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@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 >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> >> -- >> -------------------------------------------- >> Andreia J. Amaral >> Unidade de Imunologia Clínica >> Instituto de Medicina Molecular >> Universidade de Lisboa >> email: andreiaamaral@fm.ul.pt >> andreia.fonseca@gmail.com >> > > > > -- > -------------------------------------------- > Andreia J. Amaral > Unidade de Imunologia Clínica > Instituto de Medicina Molecular > Universidade de Lisboa > email: andreiaamaral@fm.ul.pt > andreia.fonseca@gmail.com > -- -------------------------------------------- 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]]