Hello, I am new to snp array and I am trying to work on affymetrix's SNP6.0 data through oligo package. But I couldn't find a way to either get the copy number or get the data into oligoSnpSet object: library(oligo) fullFilenames <- list.celfiles(path=getwd(),full.name=TRUE) #normalization and summarization data <- just SNPRMA(fullFilenames) #genotype calling outputDir <- file.path(getwd(),'crlmmTest') crlmm(fullFilenames,outputDir) crlmmOut <-getCrlmmSummaries(outputDir) >data SnpCnvQSet (storageMode: lockedEnvironment) assayData: 906600 features, 7 samples element names: thetaA, thetaB phenoData sampleNames: CA_SNP_Array_6_Gist194.CEL, CA_SNP_Array_6_Gist237_11.CEL, ..., C A_SNP_Array_6_Gist363_2.CEL (7 total) varLabels and varMetadata description: none featureData featureNames: SNP_A-1780270, SNP_A-1780271, ..., SNP_A-8717615 (906600 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: pd.genomewidesnp.6 > crlmmOut SnpCnvCallSetPlus (storageMode: lockedEnvironment) assayData: 906600 features, 7 samples element names: calls, callsConfidence, thetaA, thetaB phenoData sampleNames: CA_SNP_Array_6_Gist194.CEL, CA_SNP_Array_6_Gist237_11.CEL, ..., C A_SNP_Array_6_Gist363_2.CEL (7 total) varLabels and varMetadata description: none featureData featureNames: SNP_A-4270094, SNP_A-8282305, ..., SNP_A-8433021 (906600 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: pd.genomewidesnp.6 Am I doing something Wrong? Have I missed anything? Thanks, Yupu