Hi Pedro,

Yes you're right.

I used vsn just cause it transform directly in log2. But I should do with
method="quantile" and than use
MA<-log2(MA)

or better:

MA <- normalizeBetweenArrays(log2( Gbg.sort$G), method="quantile")

I've just try it and the result are slightly different, apparently it's
better. And in fact in the case of miRNA is good to not make assumptions
about the expression of the majority of the genes. we have 490 x 20 miRNA
plus few hundreds of controls, is really different from the situation of a
microarray for gene expression.

Thanks for the correction.

Francesco
--

Cancer Genomics Lab.
"Edo e Elvo Tempia" Foundation.
Via Malta 3 13900 Biella
Tel +39 015351830
http://www.fondoedotempia.it/sub_lab.php

2007/7/30, Pedro López-Romero <plopez@cnic.es>:
>
> Hi Francesco,
>
> This is not an answer to what you've asked but an additional question. Do
> you think that it's correct to apply a vsn normalization for a miRNA
> chip?.
> Vsn assumes that the majority of the genes are not differetially
> expressed,
> and this might not be the case for a microRNA chip.
>
> Thanks
>
> Pedro.
>

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