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


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