[BioC] oligo package - affymetrix tiling arrays.

[Lavinia Gordon]

   Dear all
   I  would like to use the oligo package on my Affymetrix human promoter
   arrays.
   I  am using the following code, based on the BioC2007-oligo code and a
   posting by Ann Hess on 20/07/2008.
   >library(oligo)
   > 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
   "TilingFeatureSet"
   > is(AllArrays)
   [1]         "TilingFeatureSet"        "FeatureSet"              "eSet"
   "VersionedBiobase"
   [5] "Versioned"
   > sessionInfo()
   R version 2.7.0 (2008-04-22)
   x86_64-redhat-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_ADD
   RESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
   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
   pmPosition
   pmOffset
   or chromosome()
   Any advice greatly appreciated.
   with regards
   Lavinia Gordon.

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