I am trying to use the beadarray package with some beadlevel data I have. The problem occurs when I try to create bead summary data : BLData = readIllumina(arrayNames = targets$arrayID, path = "./rawdata", targets = targets, backgroundMethod="none", useImage=FALSE,annoPkg="Humanv3" ) BLData.bc = backgroundCorrect(BLData) BSData = createBeadSummaryData(BLData.bc, imagesPerArray = 1) Error in .nextMethod(e1, e2) : comparison of these types is not implemented I see others have posted messages about this error using other packages, and that a possible explanation is that the objects aren't what we think they are.. So summary of the input object tells me that I have a BeadLevelList, which is what I think I should have.. so really don't get why this doesn't work.. summary(BLData.bc) Length Class Mode 1 BeadLevelList S4 I have tried using both beadarray_1.10.0 and version 1.11.5, with R 2.8.1 I have listed sessionInfo and traceback underneath. Does anyone have any idea about why this happens? Or what I need to do to get it to work? Thanks, Anne-Kristin Stavrum University of Bergen, Norway > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_1.11.5 sma_0.5.15 hwriter_1.1 geneplotter_1.12.0 [5] annotate_1.12.1 Biobase_1.12.2 limma_2.9.13 loaded via a namespace (and not attached): [1] AnnotationDbi_1.4.3 DBI_0.2-4 KernSmooth_2.22-22 [4] RColorBrewer_0.2-3 RSQLite_0.7-1 traceback() 34: eval(expr, envir, enclos) 33: eval(call, callEnv) 32: callNextMethod(e1, e2) 31: classVersion(object)[names(vers)] == vers 30: classVersion(object)[names(vers)] == vers 29: isCurrent(object, class(object)) 28: isCurrent(object, class(object)) 27: isCurrent(object) 26: isCurrent(object) 25: isValidVersion(object, "eSet") 24: validMsg(msg, isValidVersion(object, "eSet")) 23: validityMethod(as(object, superClass)) 22: identical(x, TRUE) 21: anyStrings(validityMethod(as(object, superClass))) 20: validObject(.Object) 19: .nextMethod(.Object, ...) 18: eval(expr, envir, enclos) 17: eval(call, callEnv) 16: callNextMethod(.Object, ...) 15: .local(.Object, ...) 14: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 13: eval(expr, envir, enclos) 12: eval(call, callEnv) 11: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 10: .local(.Object, ...) 9: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, experimentData = experimentData, annotation = annotation, featureData = featureData) 8: eval(expr, envir, enclos) 7: eval(call, callEnv) 6: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, experimentData = experimentData, annotation = annotation, featureData = featureData) 5: .local(.Object, ...) 4: initialize(value, ...) 3: initialize(value, ...) 2: new("ExpressionSetIllumina") 1: createBeadSummaryData(BLData.bc, imagesPerArray = 1)