[BioC] Help on using read.Agilent from marray library

Archana Sharma-Oates sharmaoa at bmb.leeds.ac.uk
Fri Apr 29 17:28:37 CEST 2005


I am new to R and am trying to read Agilent microarray files using
read.Agilent in the marray library.

Please see below for the R version installed on my computer

platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
major    2
minor    0.0
year     2004
month    10
day      04
language R

Please see cammand line arguments below:
data.dir is the directory path
> hcc.targets <- read.marrayInfo(file.path(data.dir, "target.text"))
> hcc.layout <- read.marrayLayout(fname=file.path(data.dir, "layout.text"),
			ngr=1, ngc=1, nsr=105, nsc=215, ctl.col=6, skip=0)
>  hcc.gnames <- read.marrayInfo(file.path(data.dir, "layout.text"),
				info_id=4:5, labels=4, skip=10)
> fnames <- dir(path=data.dir, pattern=paste("*", ".txt", sep="\."))
>hcc <- read.Agilent(fnames, path="data.dir", name.Gf="gMedianSignal",
		name.Gb="gBGMedianSignal", name.Rf = "rMedianSignal", name.Rb =
		"rBGMedianSignal", layout=hcc.layout, gnames=hcc.gnames, 			  	 	
		targets=hcc.targets, skip=10, sep="\t", quote="\"", DEBUG=TRUE)

However I am getting an error:

Error in read.Agilent(fnames, path = "data.dir", name.Gf = "gMedianSignal" ,

        Object "descript" not found

I have checked the file and there doesn't appear to be any problems opening
 it and there are no strange characters.

I am not sure what I am doing wrong or what to try next.

Can you please help?

Many thanks in advance.
Archana Sharma-Oates

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