Dear Alejandro, DEXSeq is working fine now. Thanks very much for the quick fix.
Best wishes, Leonard On Thu, Jul 30, 2015 at 9:02 AM, Alejandro Reyes <alejandro.re...@embl.de> wrote: > Dear Leonard, > > Thanks a lot for reporting this. It should be fixed in the version that I > just committed to the svn (DEXSeq 1.5.10). > > While debugging the DEXSeq code, I noticed that summarizedOverlaps is giving > me an error, which I think its a bug while creating the > summarizedExperiments object that is returned. Here a reproducible example: > >> library(GenomicRanges) >> library(GenomicFeatures) >> library(GenomicAlignments) >> >> hse <- makeTxDbFromBiomart( biomart="ensembl", > + dataset="hsapiens_gene_ensembl" ) > > > Download and preprocess the 'transcripts' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Download and preprocess the 'splicings' data frame ... OK > Download and preprocess the 'genes' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TxDb object ... OK >> >> bamDir <- system.file( > + "extdata", package="parathyroidSE", mustWork=TRUE ) >> fls <- list.files( bamDir, pattern="bam$", full=TRUE ) >> >> bamlst <- BamFileList( > + fls, index=character(), > + yieldSize=100000, obeyQname=TRUE ) >> >> exonicParts <- disjointExons( hse, aggregateGenes=FALSE ) >> >> SE <- summarizeOverlaps( exonicParts, bamlst, > + mode="Union", singleEnd=FALSE, > + ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE ) > Error in SummarizedExperiment(assays = SimpleList(counts = counts), > rowRanges = features, : > error in evaluating the argument 'assays' in selecting a method for > function 'SummarizedExperiment': Error in validObject(.Object) : > invalid class “SimpleList” object: invalid object for slot "listData" in > class "SimpleList": got class "matrix", should be or extend class "lis > t" > > And the output of sessionInfo(), > >> sessionInfo() > R Under development (unstable) (2015-07-25 r68744) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 15.04 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GenomicAlignments_1.5.12 Rsamtools_1.21.14 > [3] Biostrings_2.37.2 XVector_0.9.1 > [5] GenomicFeatures_1.21.13 AnnotationDbi_1.31.17 > [7] DEXSeq_1.15.10 DESeq2_1.9.26 > [9] RcppArmadillo_0.5.200.1.0 Rcpp_0.12.0 > [11] SummarizedExperiment_0.3.2 GenomicRanges_1.21.17 > [13] GenomeInfoDb_1.5.9 IRanges_2.3.15 > [15] S4Vectors_0.7.10 Biobase_2.29.1 > [17] BiocGenerics_0.15.3 BiocParallel_1.3.42 > > loaded via a namespace (and not attached): > [1] genefilter_1.51.0 statmod_1.4.21 locfit_1.5-9.1 > [4] reshape2_1.4.1 splines_3.3.0 lattice_0.20-33 > [7] colorspace_1.2-6 rtracklayer_1.29.12 survival_2.38-3 > [10] XML_3.98-1.3 foreign_0.8-65 DBI_0.3.1 > [13] RColorBrewer_1.1-2 lambda.r_1.1.7 plyr_1.8.3 > [16] stringr_1.0.0 zlibbioc_1.15.0 munsell_0.4.2 > [19] gtable_0.1.2 futile.logger_1.4.1 hwriter_1.3.2 > [22] latticeExtra_0.6-26 geneplotter_1.47.0 biomaRt_2.25.1 > [25] proto_0.3-10 acepack_1.3-3.3 xtable_1.7-4 > [28] scales_0.2.5 Hmisc_3.16-0 annotate_1.47.4 > [31] gridExtra_2.0.0 ggplot2_1.0.1 digest_0.6.8 > [34] stringi_0.5-5 grid_3.3.0 tools_3.3.0 > [37] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.7 > [40] RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.3 > [43] futile.options_1.0.0 MASS_7.3-43 rpart_4.1-10 > [46] nnet_7.3-10 > > > Best regards, > Alejandro Reyes > > > > > > On 29.07.2015 20:26, Leonard Goldstein wrote: > > Hi all, > > I'm having trouble creating a DEXSeqDataSet object (in the devel > version of DEXSeq) > > Running the example included in the manual page results in the same > error I get with my own data (see below) > > Many thanks for your help. > > Leonard > > library(DEXSeq) > 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( > > + paste0("gene", 1:10), > + each= 100 ) > > featureID <- rep( > > + paste0("exon", 1:10), > + times= 100 ) > > DEXSeqDataSet( countData, sampleData, design, > > + featureID, groupID ) > converting counts to integer mode > > Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) : > replacement has 1 row, data has 0 > In addition: Warning message: > In DESeqDataSet(se, design, ignoreRank = TRUE) : > 900 duplicate rownames were renamed by adding numbers > > sessionInfo() > > R version 3.2.1 (2015-06-18) > Platform: x86_64-unknown-linux-gnu (64-bit) > Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) > > 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] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] DEXSeq_1.15.9 DESeq2_1.9.26 > [3] RcppArmadillo_0.5.200.1.0 Rcpp_0.12.0 > [5] SummarizedExperiment_0.3.2 GenomicRanges_1.21.17 > [7] GenomeInfoDb_1.5.9 IRanges_2.3.15 > [9] S4Vectors_0.7.10 Biobase_2.29.1 > [11] BiocGenerics_0.15.3 BiocParallel_1.3.41 > > loaded via a namespace (and not attached): > [1] genefilter_1.51.0 statmod_1.4.21 locfit_1.5-9.1 > [4] reshape2_1.4.1 splines_3.2.1 lattice_0.20-33 > [7] colorspace_1.2-6 survival_2.38-3 XML_3.98-1.3 > [10] foreign_0.8-65 DBI_0.3.1 RColorBrewer_1.1-2 > [13] lambda.r_1.1.7 plyr_1.8.3 stringr_1.0.0 > [16] zlibbioc_1.15.0 Biostrings_2.37.2 munsell_0.4.2 > [19] gtable_0.1.2 futile.logger_1.4.1 hwriter_1.3.2 > [22] latticeExtra_0.6-26 geneplotter_1.47.0 biomaRt_2.25.1 > [25] AnnotationDbi_1.31.17 proto_0.3-10 acepack_1.3-3.3 > [28] xtable_1.7-4 scales_0.2.5 Hmisc_3.16-0 > [31] annotate_1.47.4 XVector_0.9.1 Rsamtools_1.21.14 > [34] gridExtra_2.0.0 ggplot2_1.0.1 digest_0.6.8 > [37] stringi_0.5-5 grid_3.2.1 tools_3.2.1 > [40] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.7 > [43] RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.3 > [46] futile.options_1.0.0 MASS_7.3-43 rpart_4.1-10 > [49] compiler_3.2.1 nnet_7.3-10 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel