[BioC] oligo package - affymetrix tiling arrays.

[Mark Robinson]

Hey Lavinia.

I get the same error as you ... but below is an alternative way to  
access the chromosome position of the probes.

 > rd1<-read.celfiles(fn[1:2],pkgname="pd.hs.prompr.v02.3.ncbiv36")
 > pd1<-getPD(rd1)
 > pd1
Class........: platformDesign
Manufacturer.: Affymetrix
Genome Build.: hg18
Error in geometry(object) :
   no slot of name "geometry" for this object of class "platformDesign"

 > dim(rd1)
Features  Samples
  4347375        2
 > length(pd1$feature_type)
[1] 4347375

 > pd1$feature_type[100000:100010]
  [1] PM PM PM PM PM PM PM PM PM PM PM
Levels: MM PM
 > pd1$position[100000:100010]
  [1] 100611443 100611473  10061152 100611521 100611553 100611590  
100611626
  [8] 100611650 100611685  10061171 100611715
 > pd1$chromosome[100000:100010]
  [1] chr9 chr9 chr4 chr9 chr9 chr7 chr7 chr7 chr9 chr2 chr9
24 Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10  
chr11 ... chrY


Cheers,
Mark



On 01/08/2008, at 12:24 PM, Lavinia Gordon wrote:

>
>   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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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852