Yes, here it is:
samr.obj<-samr(data,resp.type="Two class unpaired", nperms=100,
center.arrays=T)

where *data *is a matrix of microarray gene expressions with genes as rows
and tissues as columns. With putting *center.arrays=T *the *data* matrix is
normalized such as each column has median=0. I would like to retrieve the
new normalized matrix, but it seems that it is not returned by *samr.* If
you have any idea on how I can find this transformed matrix I would be glad
to hear that!

Thanks again,
E.



On Tue, Jun 10, 2008 at 11:30 PM, Richardson, Patrick <
Patrick.Richardson@vai.org> wrote:

> Could you post your code so we can see what you are trying to do?
>
> Thanks,
>
> Patrick
>
> ________________________________________
> From: r-help-bounces@r-project.org [r-help-bounces@r-project.org] On
> Behalf Of Eleni Christodoulou [elenichri@gmail.com]
> Sent: Tuesday, June 10, 2008 11:20 AM
> To: r-help@r-project.org
> Subject: [R] samr result
>
> Hello list!
>
> I have a proble trying to perform a SAM analysis using the function samr
> from the samr package. I have put the option *center.arrays=TRUE *in order
> to scale all the experiments to median=0. I would like to retrieved the
> scaled data but it seems that samr does not return it...Does anyone have
> any
> idea on this?
>
> Thanks a lot!!!
> E.
>
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