Wolfgang -- Thanks for the report! This problem, which only affected users of the 'development' version of R from the last several days, is fixed in the development version of Biobase 1.15.31. Martin Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > ... this seems to have crept in recently. my first guess would be it has > to do with either Biobase or methods; for example: > > > library("affydata") > data("Dilution") > options(error=recover) > rma(Dilution) > > > Background correcting > Normalizing > Calculating Expression > > Error in .nextMethod(e1, e2) : comparison of these types is not implemented > > Enter a frame number, or 0 to exit > > 1: source("test.R") > 2: eval.with.vis(ei, envir) > 3: eval.with.vis(expr, envir, enclos) > 4: rma(Dilution) > 5: new("ExpressionSet", phenoData = phenoData(object), annotation = > annotation > 6: initialize(value, ...) > 7: initialize(value, ...) > 8: .local(.Object, ...) > 9: callNextMethod(.Object, phenoData = phenoData, featureData = > featureData, e > 10: eval(call, callEnv) > 11: eval(expr, envir, enclos) > 12: .nextMethod(.Object, phenoData = phenoData, featureData = > featureData, expe > 13: .local(.Object, ...) > 14: callNextMethod(.Object, assayData = assayData, phenoData = > phenoData, featu > 15: eval(call, callEnv) > 16: eval(expr, envir, enclos) > 17: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureD > 18: .local(.Object, ...) > 19: callNextMethod(.Object, ...) > 20: eval(call, callEnv) > 21: eval(expr, envir, enclos) > 22: .nextMethod(.Object, ...) > 23: validObject(.Object) > 24: anyStrings(validityMethod(as(object, superClass))) > 25: identical(x, TRUE) > 26: validityMethod(as(object, superClass)) > 27: validMsg(NULL, isValidVersion(object, "eSet")) > 28: isValidVersion(object, "eSet") > 29: isCurrent(object) > 30: isCurrent(object) > 31: isCurrent(object, class(object)) > 32: isCurrent(object, class(object)) > 33: classVersion(object)[names(vers)] == vers > 34: classVersion(object)[names(vers)] == vers > 35: callNextMethod(e1, e2) > 36: eval(call, callEnv) > 37: eval(expr, envir, enclos) > > Selezione: > > >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-09-04 r42759) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_ IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_I T.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] hgu95av2cdf_1.17.0 affydata_1.11.2 affy_1.15.7 > [4] preprocessCore_0.99.12 affyio_1.5.8 Biobase_1.15.30 > [7] fortunes_1.3-3 > > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > _______________________________________________ > 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 Bioconductor / Computational Biology http://bioconductor.org