Thanks Pedro,

You are probably right again.
So you suggest to do :

MA <- normalizeBetweenArrays(log2( Gbg.sort$G), method="none")

I tougth quantile normalisation adjust just intensities between arrays. I'm
looking for further documentation about normalisationBetweenArrays and
related methods.

A comparation of plot MA between method="none", method="quantile" and
method="vsn" reveals that quantile normalisation effects less than vsn
normalisation (rispectively against "none"). With method="none" anyway the
spot are more differentially expressed. And this is a good point.

Francesco

2007/7/30, Pedro López-Romero <plopez@cnic.es>:
>
>
>
> Hi Francesco,
>
>
>
> Don't you think that (for the miRNA data) the quantile method might have
> the same problem as the vsn method has, i.e, the assumption that the
> majority of the genes do not show differential expression among experimental
> conditions? I think that using vsn or quantile method for normalizing
> between miRNA chips could introduce strong artifacts in the data.
>
>
>
> Pedro.-
>



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