[BioC] problems about cDNA vs genomic arrays normalization

[Wolfgang Huber]

Dear Yanju,

you can calculate the log-ratios for each array, and then normalize the
log-ratios between arrays by assuming that the majority of these have
negligible changes (e.g. quantile normalization or just scaling). That
should still be a viable assumption in your case.

Afais there is no simple answer on how this compares with Jenny's
proposition (i.e. how to judge what is "best"), but you can do an
evaluation of the bottom-line result using alternative preprocessing
strategies and see where you get best results.

You might also want to try to get your biologists talk to you already
before doing the experiments, on the experimental design.

 Best wishes
 Wolfgang
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

> Dear all,
> 
> I have got a microarray dataset derived from common reference design. 
> The common reference is gemoic DNA.  In normal normalization, we assume 
> that  large fraction of genes is not differently expressed, then the 
> adjustment strategies are used to let the log-ratios have a median(mean) 
> of 0. But in my case, every spot would have the same observed signal in 
> the genomic channel while the signals in the cDNA channel vary greatly. 
> Therefore, the strategies that i just mentioned are not suitable. I was 
> wondering how to normalize this kinds of data? Is that any packages or 
> functions existed already? Expecting your reply.
> 
> Regards,
> Yanju
>