[BioC] rma() error

Jose Duarte jose.duarte at human-anatomy.oxford.ac.uk
Tue Apr 6 15:49:23 CEST 2004

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
bgcorrect.methods <- c(bgcorrect.methods, "gcrma")
normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")
express.summary.stat.methods <- c(express.summary.stat.methods, "rlm")
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
	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

Any ideas what the error means or what might be happening here? (I'm on
RedHat9, R 1.8.1, affy 1.3.28)



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