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Question: Annotating Results for HuEx 1.0 STv2 - Oligo
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gravatar for Bade
4.2 years ago by
Bade310
Delaware
Bade310 wrote:
Hi All, I am using Oligo package to analyse samples generated using HuEx 1.0 ST v2 chip. The problem I am facing is with annotating the results. Here is my code (simplified): celFilesA <- list.celfiles() AF_data.A <- read.celfiles(celFilesA,pkgname='pd.huex.1.0.st.v2') AF.eset.RMA <- rma(AF_data.A,target='core') > dim(exprs(AF.eset.RMA)) [1] 22011 10 ##Attempt to annotate library(biomaRt) ID <- rownames(AF.eset.RMA) ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl') Anno <- getBM(attributes=c("strand","transcript_start","chromosome_name","hgnc _symbol"),filters=c("affy_huex_1_0_st_v2"),values=ID,mart=ensembl) > dim(Anno) [1] 1635 4 As you see, out of total 22011 genes/probeset I can annotate only 1635 genes/probesets. Is there any way I can get the annotations for all of the genes/probesets and add them back to my expression set (AF.eset.RMA). So, that annotations are included in the final results. Usually, with other chips I do this: ID <- featureNames(AF.eset.RMA) Symbol <- getSYMBOL(ID, 'mouse4302.db') Name <- as.character(lookUp(ID, "mouse4302.db", "GENENAME")) tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name,stringsAsFactors=F) tmp[tmp=="NA"] <- NA fData(AF.esetRMA) <- tmp And this is what I want to achieve in present case. I would appreciate your help. Thanks AK
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