Hi Anne-Kristin -- Anne-Kristin Stavrum <anne-kristin.stavrum at="" med.uib.no=""> writes: > 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? your packages are a real mix -- beadarray 1.11.5 is from the development branch, Biobase 1.12.2 is from several years ago, I think. The place to start is to bring some sense to this, at least updating installed packages as described on http://bioconductor.org/docs/install/ but since you're using the devel. version of beadarray then perhaps what you want is to use the devel. version of R and the devel. version of Bioconductor packages, e.g., install the devel version of R, then > source('http://bioconductor.org/biocLite.R') > biocLite('beadarray') For what it's worth it appears from the traceback that > 2: new("ExpressionSetIllumina") causes the problem on your system. This succeeds with the sessionInfo as below... > sessionInfo() R version 2.8.1 Patched (2009-03-27 r48262) x86_64-unknown-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_1.10.0 sma_0.5.15 hwriter_1.1 [4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [7] AnnotationDbi_1.4.2 lattice_0.17-20 Biobase_2.2.2 [10] limma_2.16.5 loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.1 KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RSQLite_0.7-1 is deep within Biobase; it could be that your object is quite outdated; have you tried updateObject() or recreating it? > 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 _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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