[BioC] question on easyRNASeq developer version

[Nicolas Delhomme]

Dear Yanju, René,

I tracked down the error to a Bioc package I depend on. The Bioc developer are working on it now and they'll let me know as soon as they come up with a solution. The good news being that they identified the issue, the bad one being that it might take some time to fix. In the meanwhile, I'll try to come up with a decent work-around. I'll keep you posted.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Sep 21, 2012, at 5:54 PM, Yanju Zhang wrote:

> Hi Nico,
> 
> It is fine with me to upload my bam file. Please give me the link.
> 
> Best wishes
> Yanju
> 
> Code + error + sessionInfo
> > chr.sizes=as.list(seqlengths(Hsapiens))
> > bamfiles=dir(getwd(),pattern="*.sorted.bam$")
> > RNASeq<- easyRNASeq(filesDirectory=getwd(),
> +                     organism="Hsapiens",
> +                     chr.sizes=chr.sizes,
> +                     #readLength=80L,
> +                     annotationMethod="biomaRt",
> +                     format="bam",
> +                     count="genes",
> +                     summarization="geneModels",
> +                     filenames=bamfiles[1],
> +                     outputFormat="RNAseq"
> +                     )
> 
> 
> 
> Checking arguments... 
> Fetching annotations... 
> Computing gene models... 
> Summarizing counts... 
> Processing test.sorted.bam 
> Updating the read length information. 
> The reads have been trimmed. 
> Minimum length of 50 bp. 
> Maximum length of 80 bp. 
> Error in mk_singleBracketReplacementValue(x, value) : 
>   'value' must be a CompressedIntegerList object
> In addition: Warning messages:
> 1: The use of the list for providing chromosome sizes has been deprecated. Use a named numeric vector instead. 
> 2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes,  :
>   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?
> 3: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>   You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
> 4: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>   Not all the chromosome names in your chromosome size list 'chr.sizes' are present in your read file(s) (aln or bam).
> 5: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter,  :
>   The available chromosomes in both your read file(s) (aln or bam) and 'chr.sizes' list were restricted to their common term.
> These are: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY.
> 
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
>  [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.3.14                 
>  [3] ShortRead_1.15.11                  latticeExtra_0.6-24               
>  [5] RColorBrewer_1.0-5                 Rsamtools_1.9.30                  
>  [7] DESeq_1.9.14                       lattice_0.20-6                    
>  [9] locfit_1.5-8                       BSgenome_1.25.8                   
> [11] GenomicRanges_1.9.65               Biostrings_2.25.12                
> [13] IRanges_1.15.44                    edgeR_2.99.8                      
> [15] limma_3.12.1                       biomaRt_2.13.2                    
> [17] Biobase_2.17.7                     genomeIntervals_1.13.3            
> [19] BiocGenerics_0.3.1                 intervals_0.13.3                  
> 
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.18.1 DBI_0.2-5            RCurl_1.91-1        
>  [4] RSQLite_0.11.1       XML_3.9-4            annotate_1.34.1     
>  [7] bitops_1.0-4.1       genefilter_1.38.0    geneplotter_1.35.1  
> [10] grid_2.15.1          hwriter_1.3          splines_2.15.1      
> [13] stats4_2.15.1        survival_2.36-14     xtable_1.7-0        
> [16] zlibbioc_1.2.0 
> 
> 
> 
> 
> On 21 September 2012 16:37, Nicolas Delhomme <delhomme at embl.de> wrote:
> Hi Yanju,
> 
> Would you be OK with uploading the file that creates the problem on my dropbox? If that's OK, I'll send you a link to it. That would be best for me to reproduce the error.
> 
> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Genome Biology Computational Support
> 
> European Molecular Biology Laboratory
> 
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
> 
> 
> 
> 
> 
> On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote:
> 
> > Hi Nico
> > As mentioned in SEQAnswers, I also encountered this problem:
> > > "Error in mk_singleBracketReplacementValue(x, value) :
> > > 'value' must be a CompressedIntegerList object"
> >
> > In my bam files, the reads are with different length.
> >
> > I am expecting the solution. If you need more information, please let me know.
> >
> >
> > Best wishes
> > Yanju
> >
> >
> 
>