[BioC] oligo package - affymetrix tiling arrays.
Mark Robinson
mrobinson at wehi.EDU.AU
Fri Aug 1 04:35:29 CEST 2008
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
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