Hi list, I am having trouble trying to annotate a Human Exon 1.0 ST expression set. I know little about R and bioconductor and I find it hard to understand the instructions I find on the web. When analyzing HGU 133 Plus 2.0 arrays, I just had to follow these instructions: library("hgu133plus2.db") symbol <- hgu133plus2SYMBOL genename <- hgu133plus2GENENAME symbols <- unlist(as.list(hgu133plus2SYMBOL)) genenames <- unlist(as.list(hgu133plus2GENENAME)) results <- cbind(symbols,genenames,exprs.eset) And the ???results??? would be the expression matrix with genenames and genesymbols associated to each affymetrix gene ID. I am trying to get the same results (the same matrix) for the Human Exon chip. I have summarized my data to the gene level using the oligo package and created the expression matrix: geneSummaries <- rma(abatch.raw, target="core") expressionMatrix <- exprs (geneSummaries) Now I understand that the best option is to use the biomaRt package to annotate, I have been reading the vignette but I am completely lost as for what I should do to just attach genenames, symbols, or some other identifier to the expression matrix. Could somebody tell me which commands or which steps I should follow? Thank you very much -- output of sessionInfo(): no sessioninfo -- Sent via the guest posting facility at bioconductor.org.

I wonder if an annotation package used by oneChannelGUI could be useful to you. The packages: HuExExonProbesetLocation,MoExExonProbesetLocation andRaExExonProbesetLocation are derived by Affymetrix data annotation and contains the following info: library(HuExExonProbesetLocation) as.data.frame(HuExExonProbesetLocation[1:3,]) EPROBESETID CHR STRAND START STOP GPROBESETID ANNLEVEL 2315101 chr1 + 11925 12167 2315100 extended 2315102 chr1 + 12657 12692 2315100 extended 2315104 chr1 + 13366 13888 2315100 extended ... Gene level annotation can be generated using the stand alone function standAloneBuildingLocalAnnotation present in oneChannelGUI package. This annotation provides the following info: "PROBESETID","ACC","SYMBOL","DESCRIPTION","CYTOBAND" Annotation can also be added to a data frame using the stand alone function: standAloneAddingAnnotation library(oneChannelGUI) ?standAloneBuildingLocalAnnotation standAloneBuildingLocalAnnotationpackage:oneChannelGUI R Documentation Creates a data frame with gene-level annotation data for exon arrays using the netaffx database Description: Standalone oneChannelGUI function to create gene-level annotation data using netaffx database. Usage: standAloneBuildingLocalAnnotation(libDirLocation = getwd(), netaffxUser = "myemail@somewhere.org", netaffxUserPw = "yourpassword", whichAnnotation = c("HuEx", "MoEx", "RaEx")) Arguments: libDirLocation: Folder where to save the annotation object netaffxUser: The email registered to Affymetrix netaffx web site netaffxUserPw: The password to access to netaffx whichAnnotation: Which annotation table should be used Value: Location of the annotation data frame. ?standAloneAddingAnnotation standAloneAddingAnnotation package:oneChannelGUI R Documentation Attach to a data frame containing gene-level data derived from Affymetrix exon arrays the annotations derived by netaffx Description: Standalone oneChannelGUI function attaches gene-level annotation to a data frame. Usage: standAloneAddingAnnotation(annotationdf, df.tobe.annotated, ids.column) Arguments: annotationdf: An annotation data frame generated with standAloneBuildingLocalAnnotation function df.tobe.annotated: A data frame containing a gene-level data of any type. It is mandatory that onne of the column contains gene-level ids ids.column: the column of the df.tobe.annotated containing gene-level ids Value: A data frame. Cheers Raf -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero@unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it [[alternative HTML version deleted]]

The contents of the Affymetrix annotation files are made available for you via: netaffx = getNetAffx(geneSummaries, 'transcript') pData(netaffx)[1:3, 1:2] but you'll most likely need to parse the resulting data, as affymetrix does not provide parsed files. :( b 2013/5/18 Laura [guest] <guest at="" bioconductor.org="">: > > Hi list, > > I am having trouble trying to annotate a Human Exon 1.0 ST expression set. I know little about R and bioconductor and I find it hard to understand the instructions I find on the web. > > When analyzing HGU 133 Plus 2.0 arrays, I just had to follow these instructions: > library("hgu133plus2.db") > symbol <- hgu133plus2SYMBOL > genename <- hgu133plus2GENENAME > symbols <- unlist(as.list(hgu133plus2SYMBOL)) > genenames <- unlist(as.list(hgu133plus2GENENAME)) > results <- cbind(symbols,genenames,exprs.eset) > And the ???results?? would be the expression matrix with genenames and genesymbols associated to each affymetrix gene ID. I am trying to get the same results (the same matrix) for the Human Exon chip. > > I have summarized my data to the gene level using the oligo package and created the expression matrix: > > geneSummaries <- rma(abatch.raw, target="core") > expressionMatrix <- exprs (geneSummaries) > > Now I understand that the best option is to use the biomaRt package to annotate, I have been reading the vignette but I am completely lost as for what I should do to just attach genenames, symbols, or some other identifier to the expression matrix. > > Could somebody tell me which commands or which steps I should follow? > > Thank you very much > > -- output of sessionInfo(): > > no sessioninfo > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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