Hi,

I am encountering an error when attempting to retrieve data from the X chromosome using GViz.  The error is unclear to me and I would greatly appreciate some help.

The code and error and sessionInfo() are below.  Please note that I have tried the code with and without ucscChromosomeNames=FALSE.

Thank you very much.

best wishes,
Chris

CODE:
##################################################
library("Gviz")
library("GenomicRanges")
library("biomaRt")
library("BiocGenerics")
ensembl67 =useMart(host='may2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL') #uses ensemble67 build ("may2012.archive.ensembl.org")
ensembl67 = useDataset("mmusculus_gene_ensembl", mart=ensembl67)
biomTrack <- BiomartGeneRegionTrack(genome = "mm9", biomart = ensembl67, chromosome = "X", start = 166123129, end = 166443668, stacking="squish", showId = TRUE, name= geneName, ucscChromosomeNames=FALSE)


ERROR:
> 	biomTrack <- BiomartGeneRegionTrack(genome = "mm9", biomart = ensembl67, chromosome = "X", start = startGene, end = endGene, stacking="squish", showId = TRUE, name= geneName, ucscChromosomeNames=FALSE)
Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x'
Please consider setting options(ucscChromosomeNames=FALSE) to allow for arbitrary chromosome identifiers.


> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_3.0.8          limma_3.14.4         biomaRt_2.14.0       GenomicRanges_1.10.7 IRanges_1.16.6       BiocGenerics_0.4.0  
[7] Gviz_1.2.1          

loaded via a namespace (and not attached):
 [1] annotate_1.36.0        AnnotationDbi_1.20.6   Biobase_2.18.0         Biostrings_2.26.3      biovizBase_1.6.2       bitops_1.0-4.2        
 [7] BSgenome_1.26.1        cluster_1.14.3         colorspace_1.2-1       DBI_0.2-5              DESeq_1.10.1           dichromat_2.0-0       
[13] genefilter_1.40.0      geneplotter_1.36.0     GenomicFeatures_1.10.2 Hmisc_3.10-1           labeling_0.1           lattice_0.20-13       
[19] munsell_0.4            parallel_2.15.2        plyr_1.8               RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.10.2      
[25] RSQLite_0.11.2         rtracklayer_1.18.2     scales_0.2.3           splines_2.15.2         stats4_2.15.2          stringr_0.6.2         
[31] survival_2.37-4        tools_2.15.2           XML_3.95-0.2           xtable_1.7-1           zlibbioc_1.4.0        



Christopher Gregg, PhD.
New York Stem Cell Foundation-Robertson Investigator
Assistant Professor, Neurobiology and Anatomy
Adjunct Assistant Professor, Human Genetics
323 Wintrobe Bldg 530
University of Utah, School of Medicine
20 North 1900 East
Salt Lake City, Utah 84132-3401

phone: (801) 581-8212
fax: (801) 585-9736
------------------------------------
Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html



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