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