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. ------------------------------------------------------- Bioinformatics Department Rm SW916, 9th Floor Murdoch Children's Research Institute Royal Children's Hospital Flemington Road, Parkville Victoria 3052 Australia Tel: (+613) 8341 6221 -------------------------------------------------------

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. > > ------------------------------------------------------- > Bioinformatics Department > Rm SW916, 9th Floor > Murdoch Children's Research Institute > Royal Children's Hospital > Flemington Road, Parkville > Victoria 3052 > Australia > Tel: (+613) 8341 6221 > ------------------------------------------------------- > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ 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