[BioC] Cannot receive data tracks back rtracklayer session

[tholzman at fhcrc.org]

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".

> 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