[R] Help on using read.Agilent
Archana Sharma-Oates
sharmaoa at bmb.leeds.ac.uk
Fri Apr 29 16:00:22 CEST 2005
Hello
I am new to R and am trying to read Agilent microarray files using
read.Agilent in the marray library.
Please see cammand line arguments below:
> 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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