[BioC] Using ChromHeatMap with the org.Mm.eg library

Michael Muratet mmuratet at hudsonalpha.org
Thu Aug 19 18:15:50 CEST 2010


I am attempting to make a ChromHeatMap from RNA-seq data with Entrez  
IDs using org.Mm.eg for annotation. The original data was aligned to  
the UCSC knownGenes table and I can map the original identifiers to  
just about any other system using the browser tables. I tried

 > chrData <- makeChrStrandData(matrix(neuro.ca.7d), lib="org.Mm.eg")
Error in makeChrStrandData(matrix(neuro.ca.7d), lib = "org.Mm.eg") :
   Error: Data matrix must have row names corresponding to probe IDs.

I suspect that I'm missing a step somewhere but I can't find it in the  
documentation. Is there a way to get the annotation from the org.Mm.eg  



Session info:

R version 2.11.0 (2010-04-22)

[1] en_US.UTF-8/en_US.UTF-8/C/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] ChromHeatMap_1.2.0                 hgu95av2.db_2.4.1
  [3] org.Hs.eg.db_2.4.1                 ALL_1.4.7
  [5] org.Mm.eg.db_2.4.1                 RSQLite_0.8-4
  [7] DBI_0.2-5                           
  [9] BSgenome_1.16.5                    Biostrings_2.16.7
[11] GenomicRanges_1.0.5                IRanges_1.6.8
[13] vsn_3.16.0                         limma_3.4.4
[15] gplots_2.7.4                       caTools_1.10
[17] bitops_1.0-4.1                     gdata_2.7.1
[19] gtools_2.6.1                       DESeq_1.0.4
[21] locfit_1.5-6                       akima_0.5-4
[23] geneplotter_1.26.0                 lattice_0.18-5
[25] annotate_1.26.1                    AnnotationDbi_1.10.0
[27] Biobase_2.8.0

loaded via a namespace (and not attached):
  [1] affy_1.26.1           affyio_1.16.0          
genefilter_1.30.0     preprocessCore_1.10.0
  [5] RColorBrewer_1.0-2    RCurl_1.3-1            
rtracklayer_1.8.1     splines_2.11.0
  [9] survival_2.35-8       tools_2.11.0           
XML_2.8-1             xtable_1.5-6

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806

More information about the Bioconductor mailing list