[BioC] gcrma()/rma() error

[Michael Seewald]

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
>
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