Question: error in "count" for SummarizedExperiment in easyRNASeq
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gravatar for Lescai, Francesco
5.6 years ago by
Denmark
Lescai, Francesco380 wrote:
Hi guys, I'm trying to use the function "count" in easyRNASeq to get a SummarizedExp to be used with DESeq2. I'm aware it's in active development, so just flagging this up in case I'm just doing something wrong Here's what I've done bamfiles<-dir("RNAseq/BAM files/", pattern="bam$") conditions <- c(rep("treated",8),rep("normal",8)) names(conditions) <- bamfiles rawCounts <- count(filesDirectory="RNAseq/BAM files/", pattern="bam$", organism="Mmusculus", annotationMethod="gtf", annotationFile="RNAseq/BAM files/Mus_musculus.GRCm38.72.gtf", count="genes", summarization="geneModels", conditions=conditions ) Checking arguments... Fetching annotations... Read 1142508 records Computing gene models... Summarizing counts... Processing Tophat2R1BAM.bam Updating the read length information. The reads are of 49 bp. [ ] Processing Tophat2W8BAM.bam Updating the read length information. The reads are of 49 bp. Preparing output Error in validObject(.Object) : invalid class “SummarizedExperiment” object: 'rowData' length differs from 'assays' nrow Any clues about this error? My session info below. thanks very much, Francesco > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.0.19 RcppArmadillo_0.3.910.0 Rcpp_0.10.4 easyRNASeq_1.6.0 ShortRead_1.18.0 latticeExtra_0.6-26 RColorBrewer_1.0-5 [8] Rsamtools_1.12.4 DESeq_1.12.1 lattice_0.20-23 locfit_1.5-9.1 BSgenome_1.28.0 GenomicRanges_1.12.5 Biostrings_2.28.0 [15] IRanges_1.18.3 edgeR_3.2.4 limma_3.16.7 biomaRt_2.16.0 Biobase_2.20.1 genomeIntervals_1.16.0 BiocGenerics_0.6.0 [22] intervals_0.14.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationDbi_1.22.6 bitops_1.0-6 DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.1 hwriter_1.3 [9] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 [17] zlibbioc_1.6.0 ________________________________ [[alternative HTML version deleted]]
easyrnaseq deseq2 • 618 views
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