Dear Hatice, Please ignore my previous e-mail, I misunderstood the problem! You were right, the function was (incorrectly) throwing an error if the rownames of the count matrix were NULL. I fixed this issue in the latest version in the svn. Best regards, Alejandro > Dear Hatice, > > The error is probably because the dimension of your input objects does > not match... You have to make sure that the length of the groupIDs and > featureIDs coresponds to the number of rows of your count matrix. You > also have to make sure that the number of rows of your sampleData > data.frame corresponds to the number of columns of your count data. > > Do you know if this is the case? > > Best regards, > Alejandro > >> Hello, >> >> First of all, thank you for developing and maintaining this great >> package. >> >> I am trying to create DEXSeqDataSet by following the example from manual. >> >> countData <- matrix( rpois(10000, 100), nrow=1000 ) >> sampleData <- data.frame( >> condition=rep( c("untreated", "treated"), each=5 ) ) >> design <- formula( ~ sample + exon + condition:exon ) >> groupID <- rep( >> sprintf("gene >> each= 100 ) >> featureID <- rep( >> sprintf("exon >> times= 100 ) >> DEXSeqDataSet( countData, sampleData, design, >> featureID, groupID ) >> >> There is something missing regarding to featureID and groupID. >> >> For my code >> library(DEXSeq) >> library(parallel) >> #newData <- >> data[,c(which(Basal.index),which(Her2.index),which(LumA.index),whic h(LumB.index))] >> >> condition = >> c(rep('LumA',length(which(LumA.index))),rep('LumB',length(which(Lum B.index)))) >> >> newData <- data[,c(which(LumA.index),which(LumB.index))] >> newData <- sapply(newData, as.numeric) >> # > dim(newData) >> # [1] 224158 357 >> #cds = newExonCountSet(newData, condition, gene.ids, exon.ids ) >> design <- formula( ~ sample + exon + condition:exon ) >> sampleData = data.frame(condition) >> rownames(sampleData) <- colnames(newData) >> featureID = exon.ids >> groupID = gene.ids >> cds = DEXSeqDataSet(newData, sampleData, >> design, >> featureID, groupID) >> >> But always receiving following error: >> Error in .Method(..., deparse.level = deparse.level) : >> number of rows of matrices must match (see arg 2) >> >> How can I fix this error? >> >> Thank you for your assistance in advance. >> >> Best, >> Hatice >> >>> sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] DEXSeq_1.10.0 BiocParallel_0.6.0 DESeq2_1.4.1 >> [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1 >> GenomicRanges_1.16.1 >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Biobase_2.24.0 >> [10] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.42.0 AnnotationDbi_1.26.0 BatchJobs_1.2 >> [4] BBmisc_1.5 biomaRt_2.20.0 Biostrings_2.32.0 >> [7] bitops_1.0-6 brew_1.0-6 codetools_0.2-8 >> [10] DBI_0.2-7 digest_0.6.4 fail_1.2 >> [13] foreach_1.4.2 genefilter_1.46.0 geneplotter_1.42.0 >> [16] grid_3.1.0 hwriter_1.3 iterators_1.0.7 >> [19] lattice_0.20-29 locfit_1.5-9.1 plyr_1.8.1 >> [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.16.0 >> [25] RSQLite_0.11.4 sendmailR_1.1-2 splines_3.1.0 >> [28] statmod_1.4.19 stats4_3.1.0 stringr_0.6.2 >> [31] survival_2.37-7 tools_3.1.0 XML_3.98-1.1 >> [34] xtable_1.7-3 XVector_0.4.0 zlibbioc_1.10.0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor