[BioC] how to get oligoSnpSet object?

[Yupu Liang]

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