Hi, We are creating lumiBatch objects manually the following way, using matrices of data: if( !exists( "controlData" ) ) controlData <- data.frame() if( !use.beadCounts ) beadCount <- new( "matrix" ) # otherwise the object already exists if( !use.detPValues ) detectionPValue <- new( "matrix" ) # otherwise the object already exists lumiBatch <- new( "LumiBatch", exprs = signalRaw, se.exprs = beadSD, featureData = featureData, phenoData = phenoData, controlData = controlData, beadNum = beadCount, detection = detectionPValue ) lumiBatch <- lumiQ( lumiBatch ) results <- lumiExpresso( lumiBatch, verbose = TRUE, bg.correct = FALSE, bgcorrect.param = list( method = "none" ), variance.stabilize = TRUE, varianceStabilize.param = list( method = "vst" ), normalize = FALSE, normalize.param = list( method = "none" ), QC.evaluation = FALSE ) When I run this, I get the following error: Variance Stabilizing Transform method: vst Variance stabilizing ... Perform vst transformation ... No Standard Deviation correction was applied becasue of missing bead number information. Error in !assayDataValidMembers(assayData(x.lumi), "detection") : invalid argument type I assume that one of the functions called by lumiExpresso() is looking for the detection slot of the lumiBatch, but does not find it or finds it to be of the wrong type. BTW, the same error happens if I *don't* specify the detection parameter when creating the lumiBatch... How, then, should I specify "detection" in the call to new("LumiBatch",...) when detection p-values are not available and if I want to use lumi? > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=C LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.2.1 Biobase_2.10.0 Best regards, Micha? B?a?ejczyk FlexArray Lead Developer McGill University and Genome Quebec Innovation Centre http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/in dex.aspx?l=e