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@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@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
> >
> >
>
>

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