Dear useR, I use R 2.5.0 since it's release and so for no problem... to I had to re-process some data and I encounter a problem while trying to use the mas5 function from the affy package: > da.26may.mas5 <- mas5(da.26may, sc=300) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 12625 ids to be processed | | |Error in update.default(pbt) : need an object with call component In addition: Warning message: $ operator not defined for this S4 class, returning NULL in: object$call > traceback() 8: stop("need an object with call component") 7: update.default(pbt) 6: update(pbt) 5: .local(x, pmcorrect.method, summary.method, ...) 4: computeExprSet(afbatch, summary.method = summary.method, pmcorrect.method = pmcorrect.method, ids = summary.subset, summary.param = summary.param, pmcorrect.param = pmcorrect.param) 3: computeExprSet(afbatch, summary.method = summary.method, pmcorrect.method = pmcorrect.method, ids = summary.subset, summary.param = summary.param, pmcorrect.param = pmcorrect.param) 2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", normalize = FALSE, summary.method = "mas", ...) 1: mas5(da.26may, sc = 300) > sessionInfo() R version 2.5.0 Patched (2007-04-26 r41343) i386-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" "methods" "base" other attached packages: hgu95av2 hgu95av2cdf affy affyio Biobase "1.16.0" "1.16.0" "1.14.1" "1.4.0" "1.14.0" --- David Ruau Institute for Biomedical Engineering RWTH Aachen