[BioC] Re: gcrma()/rma() error

[Michael Seewald]

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 at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>