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easyRNASeq errors / experiences
Hi all,
At the moment I'm trying to set up easyRNASeq + edgeR to analyse my paired-end data using R. I'm following the easyRNASeq manual to acquire a table of read counts which can then be used as DGElist object for edgeR.
Unfortunately, I do not even get close to the point of obtaining the DGElist object, as the easyRNASeq function crashes with the following error:
Did anyone experience a similar error message yet?
My bamfiles list consists of 4 samples aligned via GSNAP and here's how I run the function itself:
I use the devel version of easyRNASeq since it supports varying read lengths.
Any help is greatly appreciated.
At the moment I'm trying to set up easyRNASeq + edgeR to analyse my paired-end data using R. I'm following the easyRNASeq manual to acquire a table of read counts which can then be used as DGElist object for edgeR.
Unfortunately, I do not even get close to the point of obtaining the DGElist object, as the easyRNASeq function crashes with the following error:
Code:
Checking arguments... Fetching annotations... Computing gene models... Summarizing counts... Processing EMC_18_alignment.bam Updating the read length information. The alignments are gapped. Minimum length of 1 bp. Maximum length of 101 bp. Error in mk_singleBracketReplacementValue(x, value) : 'value' must be a CompressedIntegerList object In addition: Warning messages: 1: In easyRNASeq(organism = "Hsapiens", annotationMethod = "biomaRt", : There are 16696 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want? 2: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
My bamfiles list consists of 4 samples aligned via GSNAP and here's how I run the function itself:
Code:
count.genes <- easyRNASeq(organism="Hsapiens",
annotationMethod="biomaRt",
gapped=TRUE, count="genes",
summarization="geneModels",
filesDirectory=getwd(),
filenames=bamfiles,
outputFormat="RNAseq")
Any help is greatly appreciated.
Code:
> sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-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=C 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] BiocInstaller_1.5.12 BSgenome.Hsapiens.UCSC.hg19_1.3.19 [3] easyRNASeq_1.3.14 ShortRead_1.15.11 [5] latticeExtra_0.6-24 RColorBrewer_1.0-5 [7] Rsamtools_1.9.30 DESeq_1.9.14 [9] lattice_0.20-10 locfit_1.5-8 [11] BSgenome_1.25.8 GenomicRanges_1.9.65 [13] Biostrings_2.25.12 IRanges_1.15.44 [15] edgeR_2.99.8 limma_3.13.20 [17] biomaRt_2.13.2 Biobase_2.17.7 [19] genomeIntervals_1.13.3 BiocGenerics_0.3.1 [21] intervals_0.13.3 loaded via a namespace (and not attached): [1] annotate_1.35.3 AnnotationDbi_1.19.37 bitops_1.0-4.1 [4] DBI_0.2-5 genefilter_1.39.0 geneplotter_1.35.1 [7] grid_2.15.1 hwriter_1.3 RCurl_1.91-1 [10] RSQLite_0.11.2 splines_2.15.1 stats4_2.15.1 [13] survival_2.36-14 tools_2.15.1 XML_3.9-4 [16] xtable_1.7-0 zlibbioc_1.3.0
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