To affylmGUI users, I have sent version 1.10.4 of affylmGUI to the current release of Bioconductor. There were three small changes as follows: 1. References to Digestion changed to Degradation. Changed Menu Item name and function names. See Bioconductor emails from Gordon Smyth/Robert Gentleman around December 6th. 2006 confirming this choice of words. 2. Fixed a bug in Normalize.R introduced in 1.10.1 - bracket misplaced as shown below: Replaced this line Try(write.table(NormalizedAffyData.exprs),file=FileName,sep="\t",quote =FALSE,col.names=NA) with Try(write.table(NormalizedAffyData.exprs,file=FileName,sep="\t",quote= FALSE,col.names=NA)) 3. Error on console when HTML report was to be created. It read: "Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found" Modify htmlreport.R replace: try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv))) with: if (exists("HTMLenv",where=".GlobalEnv",mode="environment")){ try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv))) }#end of if (exists("HTMLenv",where=".GlobalEnv",mode="environment")) I shall update tomorrow the Bioc-devel version (1.11.4) to be the same as 1.10.4 on the release version. cheers, Keith