[BioC] Limma & Imagene

James MacDonald jmacdon at med.umich.edu
Mon Oct 27 17:13:46 MET 2003

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

I would imagine that you are using an outdated version of limma that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.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "cv.vc" <cv.vc at 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
  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,

What is the problem? Thanks

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