[BioC] One-channel cDNA data

[Wolfgang Huber]

Hi David,

you can load the data into an exprSet (each column per array). If your
different samples are biologically not too different, you can normalize
e.g. with vsn. The quantile normalization should also be applicable, but I
have little experience. Probably it will then be useful to check for
print-tip- or PCR-plate effects. If they are strong, you may want do
dismiss some of the arrays or spots, or try to make corrections. Then you
may want to average (or median)  over replicate spots, or arrays. After
that, EDA, testing etc. are more or less the same as for Affymetrix data
or two-color data with reference design.

Best regards
Wolfgang


On Mon, 10 Mar 2003, DED (David George Edwards) wrote:
> We have some one-channel cDNA studies. How are these best handled in
> BioConductor? 
> Yours
> David Edwards
> 

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Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
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