I use Imagene 4.0 and Limma R package.
My source file are into R directory ... and this is my R shell:
> library(limma)
>
YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t",
as.is=
TRUE)
> YourSample
SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 1.txt 2.txt treated untreated
2 2 3.txt 4.txt treated untreated
3 3 5.txt 6.txt treated untreated
> RG<-read.maimages(slides, source="imagene")
Error in match.arg(source, c("spot", "spot.close.open", "genepix",
"quantarray")) :
ARG should be one of spot, spot.close.open, genepix,
quantarray
What is the problem? Thanks
Your error message describes the problem. You can choose one of the
following for your source: spot, spot.close.open, genepix, or
quantarray. You chose imagene, which is not in that list, hence the
error.
I would imagine that you are using an outdated version of limma that
doesn't support the imagene format. You should upgrade to the devel
version, which does.
HTH,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "cv.vc" <cv.vc@libero.it> 10/27/03 07:37AM >>>
I use Imagene 4.0 and Limma R package.
My source file are into R directory ... and this is my R shell:
> library(limma)
>
YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t",
as.is=
TRUE)
> YourSample
SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 1.txt 2.txt treated untreated
2 2 3.txt 4.txt treated untreated
3 3 5.txt 6.txt treated untreated
> RG<-read.maimages(slides, source="imagene")
Error in match.arg(source, c("spot", "spot.close.open", "genepix",
"quantarray")) :
ARG should be one of spot, spot.close.open, genepix,
quantarray
What is the problem? Thanks
_______________________________________________
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Bioconductor@stat.math.ethz.ch
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
Ciao anonymoso,
which version of limma are you using?
Is it an up-to-date one that knows about imagene?
Best regards
Wolfgang
-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax: +49 6221 42524709
Http: www.dkfz.de/abt0840/whuber
-------------------------------------
On Mon, 27 Oct 2003, cv.vc wrote:
> I use Imagene 4.0 and Limma R package.
> My source file are into R directory ... and this is my R shell:
>
> > library(limma)
> >
> YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t
",as.is=
> TRUE)
> > YourSample
> SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5
> 1 1 1.txt 2.txt treated untreated
> 2 2 3.txt 4.txt treated untreated
> 3 3 5.txt 6.txt treated untreated
> > RG<-read.maimages(slides, source="imagene")
> Error in match.arg(source, c("spot", "spot.close.open", "genepix",
> "quantarray")) :
> ARG should be one of spot, spot.close.open, genepix,
quantarray
>
> What is the problem? Thanks
>
