dear friends, I am analyzing a dataset of illumina human methylation 450k arrays. i have the output from beadstudio, but no QC file to import. i successfully imported the TAB-delimited text file exported from beadstudio by > lmdat<-methylumiR("DAT.txt") > lmdat Object Information: MethyLumiSet (storageMode: environment) assayData: 485577 features, 108 samples element names: Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Intensity, betas, methylated, pvals, unmethylated protocolData: none phenoData sampleNames: 5684819001_R01C01, 5684819001_R01C02, ..., 5729917056_R06C02 (108 total) varLabels and varMetadata description: sampleID: sampleID label: label featureData featureNames: cg00000029, cg00000108, ..., rs9839873 (485577 total) fvarLabels and fvarMetadata description: Index: NA TargetID: NA ...: ... DHS: NA (37 total) experimentData: use 'experimentData(object)' Annotation: Major Operation History: submitted finished command 1 2011-05-11 15:47:46 2011-05-11 16:05:34 methylumiR(filename = "DAT.txt") i can successfully subset features by: > lmdat[1:10,] Object Information: MethyLumiSet (storageMode: environment) assayData: 10 features, 108 samples element names: Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Intensity, betas, methylated, pvals, unmethylated protocolData: none phenoData sampleNames: 5684819001_R01C01, 5684819001_R01C02, ..., 5729917056_R06C02 (108 total) varLabels and varMetadata description: sampleID: sampleID label: label featureData featureNames: cg00000029, cg00000108, ..., cg00000622 (10 total) fvarLabels and fvarMetadata description: Index: NA TargetID: NA ...: ... DHS: NA (37 total) experimentData: use 'experimentData(object)' Annotation: Major Operation History: submitted finished command 1 2011-05-11 15:47:46 2011-05-11 16:05:34 methylumiR(filename = "DAT.txt") 2 2011-05-11 16:11:01 2011-05-11 16:11:03 Subsetting 10 features. but when i try to subset samples, i get the following error: > lmdat[,1:10] Error in function (classes, fdef, mtable) : unable to find an inherited method for function "QCdata<-", for signature "MethyLumiSet", "NULL" i am working with R 2.11 and BioC 2.7 on a 64 bit mac os x 10.6. any help is very appreciated. thank you, dario