Hi there,
I'm preparing a tutorial, therefore I sliced two RNASeq bam files from chromosome one, in order to reduce the file size.

However, when I count the reads as it follows I have an error.
thanks,
Francesco


> countDataSet <- easyRNASeq(filesDirectory=getwd(),
+                            organism="HSapiens",
+                            chr.sizes=as.list(seqlengths(Hsapiens)),
+                            readLength=100L,
+                            annotationMethod="biomaRt",
+                            format="bam",
+                            count="exons",
+                            filenames=bamfiles,
+                            normalize=TRUE,
+                            outputFormat="DESeq",
+                            conditions=conditions,
+                           fitType="local"
+                           )
Checking arguments...
Fetching annotations...
Summarizing counts...
Processing SRR349689_1.fastq.novo.new.chr1.bam
Error in FUN(c("GL000229.1", "GL000200.1", "GL000228.1", "GL000241.1",  :
  (list) object cannot be coerced to type 'integer'

I also tried selecting the chromosome with chr.sel=c("1") or chr.sel=c("chr1") but in both cases I get the error
Make sure that your file is valid, that your 'chr.sel' (if provided) contains valid values; i.e. values as found in the file, not as returned by 'RNAseq'.

The alignment has been done using the ENSEMBL reference, i.e. with chromosome listed as "1".

sessionInfo()
R Under development (unstable) (2012-01-20 r58146)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] GenomicFeatures_1.6.7              AnnotationDbi_1.17.15              easyRNASeq_1.1.5
 [4] ShortRead_1.13.13                  latticeExtra_0.6-19                RColorBrewer_1.0-5
 [7] Rsamtools_1.7.27                   genomeIntervals_1.11.0             intervals_0.13.3
[10] DESeq_1.7.6                        locfit_1.5-6                       lattice_0.20-0
[13] akima_0.5-7                        BiocInstaller_1.3.7                Biobase_2.15.3
[16] edgeR_2.5.9                        limma_3.11.11                      biomaRt_2.11.1
[19] BSgenome.Hsapiens.UCSC.hg19_1.3.17 BSgenome_1.23.2                    Biostrings_2.23.6
[22] GenomicRanges_1.7.16               IRanges_1.13.22                    BiocGenerics_0.1.4

loaded via a namespace (and not attached):
 [1] DBI_0.2-5          RCurl_1.9-5        RSQLite_0.11.1     XML_3.8-0          annotate_1.33.2
 [6] bitops_1.0-4.1     genefilter_1.37.0  geneplotter_1.33.1 grid_2.15.0        hwriter_1.3
[11] rtracklayer_1.15.7 splines_2.15.0     survival_2.36-10   tools_2.15.0       xtable_1.6-0
[16] zlibbioc_1.1.1


---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
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