Thanks for the advice. I think my confusion arose probeset vs core in rma (and an interaction between oligo and affy). The affy files do contain AGI indices, gene symbols and descriptions and I've not yet got those into the analysis, but am trying the alternatives below. Cheers Steve On 07/08/2012 01:43, Benilton Carvalho wrote: > and getNetAffx returns whatever Affymetrix provides with their > annotation files... These are quite new arrays, so it's likely that on > future releases they'll add more information. b > > On 2 August 2012 18:33, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >> Hi Stephen, >> >> It sounds like you might need to make an annotation package for your new >> platform. You can see a vignette that shows how to do that here: >> >> http://www.bioconductor.org/packages/2.10/bioc/vignettes/Annotation Dbi/inst/doc/SQLForge.pdf >> >> Please let me know if there are any other issues that crop up. >> >> >> Marc >> >> >> >> >> On 08/02/2012 09:20 AM, Stephen Rolfe wrote: >>> I have a set of files from the new Aragene-1_1-st microarrays. I am using >>> oligo to analyse these but have hit a problem with the annotation. >>> >>> I have the most up-to-date packages and don't hit any error messages. >>> However, using getNetAffx doesn't seem to add annotation data to my rma >>> normalised data set. >>> >>> The feature labels are all there and the probsetids have been set. All of >>> the other data are NA. >>> >>> >>> >>> Any insight would be much appreciated. Eventually I want to analyse the >>> data >>> in limma. >>> >>> (I tried building my own pd files using pdinfoBuilder as an alternative, >>> but >>> hit a bunch of error messages that I couldn't overcome.) >>> >>> Thanks for your help >>> >>> Steve Rolfe >>> >>> >>> >>> >>> >>> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" >>> >>> >>> >>>> library("pd.aragene.1.1.st") >>>> library(oligo) >>>> library(Biobase) >>>> celfiles<-list.celfiles() >>>> affyRaw<-read.celfiles(files=celfiles) >>> Platform design info loaded. >>> >>> Reading in : WT16HypCon1_01_A05.CEL >>> >>> Reading in : WT16HypCon2_02_A07.CEL >>> >>> Reading in : WT16HypCon3_03_B05.CEL >>> >>> Reading in : WT16HypInf1_04_B07.CEL >>> >>> Reading in : WT16HypInf2_05_C05.CEL >>> >>> Reading in : WT16HypInf3_06_C07.CEL >>> >>> Reading in : WT16RootCon1_07_D05.CEL >>> >>> Reading in : WT16RootCon2_08_D07.CEL >>> >>> Reading in : WT16RootCon3_09_E05.CEL >>> >>> Reading in : WT16RootInf1_10_E07.CEL >>> >>> Reading in : WT16RootInf2_11_F05.CEL >>> >>> Reading in : WT16RootInf3_12_F07.CEL >>> >>> Reading in : WT26HypCon1_13_H07.CEL >>> >>> Reading in : WT26HypCon2_14_G07.CEL >>> >>> Reading in : WT26HypCon3_15_H05.CEL >>> >>> Reading in : WT26HypInf1_16_G05.CEL >>> >>> Reading in : WT26HypInf2_17_A05.CEL >>> >>> Reading in : WT26HypInf3_18_A07.CEL >>> >>> Reading in : WT26RootCon1_19_B05.CEL >>> >>> Reading in : WT26RootCon2_20_B07.CEL >>> >>> Reading in : WT26RootCon3_21_C05.CEL >>> >>> Reading in : WT26RootInf1_22_C07.CEL >>> >>> Reading in : WT26RootInf2_23_D05.CEL >>> >>> Reading in : WT26RootInf3_24_D07.CEL >>> >>>> eset<-rma(affyRaw,target="core") >>> Background correcting >>> >>> Normalizing >>> >>> Calculating Expression >>> >>>> featureData(eset)<-getNetAffx(eset,"transcript") >>>> eset >>> ExpressionSet (storageMode: lockedEnvironment) >>> >>> assayData: 38408 features, 24 samples >>> >>> element names: exprs >>> >>> protocolData >>> >>> rowNames: WT16HypCon1_01_A05.CEL WT16HypCon2_02_A07.CEL ... >>> >>> WT26RootInf3_24_D07.CEL (24 total) >>> >>> varLabels: exprs dates >>> >>> varMetadata: labelDescription channel >>> >>> phenoData >>> >>> rowNames: WT16HypCon1_01_A05.CEL WT16HypCon2_02_A07.CEL ... >>> >>> WT26RootInf3_24_D07.CEL (24 total) >>> >>> varLabels: index >>> >>> varMetadata: labelDescription channel >>> >>> featureData >>> >>> featureNames: 13320001 13320003 ... 13545870 (38408 total) >>> >>> fvarLabels: transcriptclusterid probesetid ... category (18 total) >>> >>> fvarMetadata: labelDescription >>> >>> experimentData: use 'experimentData(object)' >>> >>> Annotation: pd.aragene.1.1.st >>> >>>> featureData(eset) >>> An object of class "AnnotatedDataFrame" >>> >>> rowNames: 13320001 13320003 ... 13545870 (38408 total) >>> >>> varLabels: transcriptclusterid probesetid ... category (18 total) >>> >>> varMetadata: labelDescription >>> >>>> varLabels(featureData(eset)) >>> [1] "transcriptclusterid" "probesetid" "seqname" >>> >>> [4] "strand" "start" "stop" >>> >>> [7] "totalprobes" "geneassignment" "mrnaassignment" >>> >>> [10] "swissprot" "unigene" "gobiologicalprocess" >>> >>> [13] "gocellularcomponent" "gomolecularfunction" "pathway" >>> >>> [16] "proteindomains" "crosshybtype" "category" >>> >>>> pData(featureData(eset))[1000:1002,] >>> transcriptclusterid probesetid seqname strand start stop >>> totalprobes >>> >>> 13321999 13321999 13321999<na> <na> NA NA >>> NA >>> >>> 13322001 13322001 13322001<na> <na> NA NA >>> NA >>> >>> 13322003 13322003 13322003<na> <na> NA NA >>> NA >>> >>> geneassignment >>> >>> 13321999 --- // --- // intron-exon control // --- // --- >>> >>> 13322001 --- // --- // intron-exon control // --- // --- >>> >>> 13322003 --- // --- // intron-exon control // --- // --- >>> >>> >>> mrnaassignment >>> >>> 13321999 --- // --- // intron-exon control // --- // --- // --- // --- // >>> --- // --- // >>> >>> 13322001 --- // --- // intron-exon control // --- // --- // --- // --- // >>> --- // --- // >>> >>> 13322003 --- // --- // intron-exon control // --- // --- // --- // --- // >>> --- // --- // >>> >>> swissprot unigene gobiologicalprocess gocellularcomponent >>> >>> 13321999 NA NA NA NA >>> >>> 13322001 NA NA NA NA >>> >>> 13322003 NA NA NA NA >>> >>> gomolecularfunction pathway proteindomains crosshybtype >>> >>> 13321999 NA NA NA NA >>> >>> 13322001 NA NA NA NA >>> >>> 13322003 NA NA NA NA >>> >>> category >>> >>> 13321999 normgene->intron >>> >>> 13322001 normgene->intron >>> >>> 13322003 normgene->intron >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the 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