[BioC] oligo package - affymetrix tiling arrays.

Lavinia Gordon lavinia.gordon at mcri.edu.au
Fri Aug 1 04:24:50 CEST 2008

   Dear all
   I  would like to use the oligo package on my Affymetrix human promoter
   I  am using the following code, based on the BioC2007-oligo code and a
   posting by Ann Hess on 20/07/2008.
   > library(pd.hs.prompr.v02)
   > AllArrays<-read.celfiles(list.celfiles(),pk="pd.hs.prompr.v02")
   Platform design info loaded.
   The intensity matrix will require 286.35 MB of RAM.
   > dim(pm(AllArrays))
   [1] 4243300       8
   > Pos<-pmPosition(AllArrays)
   Error in function (classes, fdef, mtable)  :
     unable to find an inherited method for function "position", for signature
   > is(AllArrays)
   [1]         "TilingFeatureSet"        "FeatureSet"              "eSet"
   [5] "Versioned"
   > sessionInfo()
   R version 2.7.0 (2008-04-22)
   attached base packages:
   [1] splines   tools     stats     graphics  grDevices utils     datasets
   [8] methods   base
   other attached packages:
   [1] pd.hs.prompr.v02_1.4.0 oligo_1.4.0            oligoClasses_1.2.0
   [4] affxparser_1.12.2      AnnotationDbi_1.2.2    preprocessCore_1.2.1
   [7] RSQLite_0.6-9          DBI_0.2-4              Biobase_2.0.1
   I am really after the chromosomal locations of the probes, but have had no
   success with
   or chromosome()
   Any advice greatly appreciated.
   with regards
   Lavinia Gordon.

   Bioinformatics Department
   Rm SW916, 9th Floor
   Murdoch Children's Research Institute
   Royal Children's Hospital
   Flemington Road, Parkville
   Victoria 3052
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