Hello Sorry if the mails seem repetitive.... I have tried to go through previous mails to track if my problem of loading the affy package has occured before and I found this mail which voices exactly the same problem that I have. This is the message I get while installing affy library: -- Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] FALSE Warning message: There is no package called 'affy' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] FALSE Warning message: There is no package called 'affydata' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, Error in getClass(Class, where = topenv(parent.frame())) : "MIAME" is not a defined class Execution halted ERROR: execution of package source for 'affyPLM' failed ** Removing '/mnt/people40c/bhowmick/RLib2/affyPLM' Broken Pipe Warning message: Installation of package affyPLM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) -- As suggested, I checked and found that 'Biobase' is properly installed and this is the output: ls("package:Biobase") [1] "$.exprSet" "$.phenoData" "Aggregate" [4] "abstract" "addNonExisting" "addPDF2Vig" [7] "addVig2Menu" "addVig4Unix" "addVig4Win" [10] "aggenv" "aggfun" "annotation" [13] "annotation<-" "as.data.frame.exprSet" "content" [16] "copyEnv" "copySubstitute" "createPackage" [19] "description" "description<-" "dumpPackTxt" [22] "env2list" "esApply" "expinfo" [25] "exprs" "exprs2excel" "exprs<-" [28] "geneNames" "geneNames<-" "getPkgVigs" [31] "hybridizations" "initfun" "iter" [34] "list2env" "locked" "multiassign" [37] "multiget" "normControls" "notes" [40] "notes<-" "openPDF" "openVignette" [43] "otherInfo" "pData" "pData<-" [46] "package.version" "phenoData" "phenoData<-" [49] "preproc" "read.MIAME" "read.exprSet" [52] "read.phenoData" "sampleNames" "samples" [55] "se.exprs" "se.exprs<-" "setOptionPdfViewer" [58] "split" "testBioCConnection" "update2MIAME" [61] "varLabels" "write.exprs" showClass("exprSet") Slots: Name: exprs se.exprs phenoData description Class: exprMatrix exprMatrix phenoData characterORMIAME Name: annotation notes Class: character character > showClass("MIAME") Slots: Name: name lab contact title Class: character character character character Name: abstract url samples hybridizations Class: character character list list Name: normControls preprocessing other Class: list list list Extends: "characterORMIAME" Wolfgang Huber wrote: > References: <1BF3BA9E-5287-11D8-90FC-000A956845CE@duke.edu> > <fe8987dc-52ad-11d8-90fc-000a956845ce@duke.edu> > > Hi Jeffrey, > > loading Biobase, and the class definitions of AffyBatch.R are really > essential for the functioning of the affy package. I don't think you can > expect to get any kind of meaningful results without these. So the > proper thing to do is to find out why Biobase doesn't install. > > When you downlonad Biobase_1.XX.tar.gz file manually and try to install, > do you get an error message, and which? What version are you using? > > If you succeed to load Biobase, can you send us the output of > > > library(Biobase) > > ls("package:Biobase") > > showClass("exprSet") > > showClass("MIAME") > > Best wishes > Wolfgang > > > Jeffrey Chang wrote: > >> I still don't know what the problem is, but I've hacked my way around >> it in a *really* ugly way. The key seems to be in the error message: >> >>> Error in getClass(Class, where = topenv(parent.frame())) : >>> "MIAME" is not a defined class >> >> I hope someone can help me with my problem... thanks Debjani -- Debjani Bhowmick Chairs of Statistics Institute of Mathematics Swiss Federal Institute of Technology(EPFL) 1015 Lausanne Switzerland Phone: +41 21 693 5596 Fax: +41 21 693 4250 .