It seems, I found the reason: When justGCRMA() is called in a subdirectory that contains the substring "GMS_AllLCM-133A_Foo" it does NOT work. When I rename it to "GMS_AllLCM-U133A_Foo" it runs fine. The "-" followed by a number is apparently interpreted in a special (numerical?) way when justGCRMA reads the CEL files from that directory. All of that applies only to the non-interactive session, it runs fine in the interactive session. Best regards, Michael On Fri, 18 Jun 2004, Michael Seewald wrote: > > Sorry, I have to correct myself. I just noted that the command fails *ONLY* in > the non-interactive environemnt, e.g. when calling a script with "source". It > works when I paste the command interactively into the R shell. This means it > behaves exactly like Jose described.. > > Best wishes, > Michael > > > On Fri, 18 Jun 2004, Michael Seewald wrote: > > > > > Dear Bioconductor people, dear Jean and Rafael, > > > > I see the same problem as Jose described (see below) with justGCRMA(). > > > > The following (while located in a directory with CEL files) does not work: > > > > > DATA.A.GCRMA<-justGCRMA(phenoData=pd) > > Computing affinities..Done. > > Adjusting for optical effect......................Done. > > Adjusting for non-specific binding.....................Done. > > Normalizing > > Calculating Expression > > Error in just.gcrma(filenames = filenames, phenoData = phenoData, description > > = description, : > > dimnames applied to non-array > > > > Splitting the task into two commands works: > > > > > DATA.A.GCRMA<-justGCRMA() > > Computing affinities..Done. > > Adjusting for optical effect......................Done. > > Adjusting for non-specific binding.....................Done. > > Normalizing > > Calculating Expression > > > phenoData(DATA.A.GCRMA) <- pd > > > > There seems to be a (non-critical) bug hidden in the code for the phenotypic > > data. By the way, doing the same with justRMA in one step works fine. > > > > Do you need more information for debugging? > > > > Regards & best wishes, > > Michael > > > > > > On Tue, 6 Apr 2004, Jose Duarte wrote: > > > > > Hi all > > > > > > I've got the file test.R with the following code: > > > > > > filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > > "1M1W050304.CEL", "1M3W050304.CEL") > > > filepath <- "/net/array/WormDystrophy" > > > samples <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > > "1M1W050304.CEL", "1M3W050304.CEL") > > > custom <- c("rma", "quantiles", "pmonly", "medianpolish") > > > log2trans <- TRUE > > > library(affy) > > > library(gcrma) > > > library(vsn) > > > bgcorrect.methods <- c(bgcorrect.methods, "gcrma") > > > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") > > > express.summary.stat.methods <- c(express.summary.stat.methods, "rlm") > > > setwd(filepath) > > > exprset <- rma(ReadAffy(filenames = filenames)) > > > > > > > > > > > > I run it in batch mode from the linux command line with "R --no- save < > > > test.R". Everything is ok, except when executing the last line. The > > > rma() runs fine with the usual output: > > > > > > Background correcting > > > Normalizing > > > Calculating Expression > > > > > > But then it comes with the error: > > > > > > Error in rma(ReadAffy(filenames = filenames)) : > > > dimnames applied to non-array > > > Execution halted > > > > > > > > > > > > This is REALLY weird because: > > > > > > 1) It runs well in an interactive session just by copying and pasting > > > the code from the test.R file > > > > > > 2) It works fine if I change the order in which the file names are > > > given!! > > > > > > > > > Any ideas what the error means or what might be happening here? (I'm on > > > RedHat9, R 1.8.1, affy 1.3.28) > > > > > > Thanks > > > > > > Jose > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > >