[BioC] RMA and quantile normalisation

[Johannes Freudenberg]

Arne,

I'd be very surprised if you'd observe a normal distribution. You should not 
rely on this assumption! I haven't seen any data yet that looked like normal 
after RMA. However, I'm not quite sure what a more appropriate distribution 
would be.

Johannes


Quoting Arne.Muller at aventis.com:

> Sorry, my last posting was incomplete (slipped over the keyboard ...).
> 
> I meant that I haven't explored other methods yet, but since the RMA
> values
> are log2, I thought that I'd get something close to a normal
> distribution.
> Comapred to a normal distribution I get many low intensity probe sets.
> 
> The values are generated like this:
> 
> eset.rma <- expresso(cel, bgcorrect.method="rma",     
>     normalize.method="quantiles", pmcorrect.method="pmonly", 
>     summary.method="medianpolish")
> 
> then:
> hist(exprs(eset.rma[,10]))
> 
> 	kind regards,
> 
> 	Arne
> 
> --
> Arne Muller, Ph.D.
> Toxicogenomics, Aventis Pharma
> arne dot muller domain=aventis com
> 
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