Hi

Sorry that I have not replied to the Bioconductor mailing list regarding the problem I had with the lumi package. I was going to do it when all the testing was done, but since I have gotten questions about my solution I will explain it now.  

I was actually giving the package the wrong file. It is many different files that Bead Studio can export and I use the GeneSpring export format. When you want to export for GeneSpring it is possible to export four different files, and it was here I did my mistake. I tried to use Probe Profiles files, but then I got at tip saying that I should use the Gene Profile files and it worked!

Another ting in the vignette for lumi is that when they make the design matrix they say that one of the arrays are to be the base line, design <- model.matrix(~ factor(sampleType)). If you do not want to use one as a base line you have to make your design matrix in another way, for example design <- model.matrix(~-1+factor(sampleType)).

Regards,
Ingrid



 
Dear Ingrid,

   I am experiencing a similar problem with error in rowname in lumiR.
What is your trick ?

Best regards
Nicolas

 
-- 
Nicolas Bertin
Researcher Bioinformatics
Genome Exploration Research Group
Genomic Sciences Center (GSC)
RIKEN Yokohama Institute 
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 
Kanagawa 230-0045 Japan

Email: nbertin@gsc.riken.jp
Phone (work): (+81)(0)45 503 9222 (extension:3116)





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