On Thu, Feb 5, 2009 at 5:02 PM, tholzman@fhcrc.org <tholzman@fhcrc.org>wrote:

> Hi,
>
> This is Ted Holzman.  I am new bioconductor user, and I have a Problem.
>
> I am using the rtracklayer package within Bioconductor.  I am trying to
> receive
> a track back from a session.  The view generated by the session looks fine
> in the browser.  But I get no data back in the track.
>
> > conservation <- trackSet(session,"Conservation")
> > conservation
> ucscTrackSet (storageMode: lockedEnvironment)
> assayData: 377 features, 1 samples
>  element names: dataVals
> phenoData
>  sampleNames: score
>  varLabels and varMetadata description: none
> featureData
>  featureNames: ., ..1, ..., ..376  (377 total)
>  fvarLabels and fvarMetadata description:
>    chrom: Chromosome ID
>    start: Start position on chromosome
>    ...: ...
>    strand: DNA strand, sense (+) or antisense (-)
>    (5 total)
> experimentData: use 'experimentData(object)'
> Annotation:
> genome: hg18
> trackLine: track name=multiz30way description=multiz30way visibility=1
>
> All this looks fine except the genome is incorrect.  It should be "mm9".
>

This would be the problem. In hg18, the scores really are zero in that
region. This part of rtracklayer has been majorly fixed up in the
development branch, but as you're a new user, you probably want to avoid
that for now.

Try calling "genomeSegment(session)" and check that the genome is mm9.
Unfortunately, I can't reproduce this, because you didn't give me all of
your code.

Thanks,
Michael


>
> > cons <- trackData(conservation)
> > head(cons)
>
>    chrom    start      end name strand  featMid score
> .   chr12 85105663 85105741    .     NA 85105702     0
> ..1 chr12 85105742 85105813    .     NA 85105778     0
> ..2 chr12 85105814 85106306    .     NA 85106060     0
> ..3 chr12 85106307 85106426    .     NA 85106366     0
> ..4 chr12 85106427 85106780    .     NA 85106604     0
> ..5 chr12 85106781 85106808    .     NA 85106794     0
>
>
> All the scores are 0!
>
> Can anybody help?
>
> Thanks,
>                -Ted
>
> ****
>
> > sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      tools     stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
> [1] GenomeGraphs_1.3.4 biomaRt_1.99.2     rtracklayer_1.2.2
> RCurl_0.94-0       Biobase_2.2.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.10.15 IRanges_1.0.9      lattice_0.17-20
> Matrix_0.999375-17 rJava_0.6-2        XML_1.99-0
>
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