Greetings Naomi,

thanks for reply. To generalize my question: when dealing with 2 sets of
samples, let's say  X1, X2, ...., Xn  and  Y1, Y2, ..., Yn,
I could run the normalization in 2 ways: A. only X(1,n) and only Y(1,n), or
B. both X(1,n),Y(1,n). Are there any a priori statistical
criteria that favors a way or the other ? If I  would take into
consideration biological criteria (the things I am interested in), the
results
from A may sometimes look better than B', or vice versa. Thanks !

Bogdan



On 11/2/07, Naomi Altman <naomi@stat.psu.edu> wrote:
>
> Dear Bogdan,
> I do not have an opinion on gcRMA versus RMA.  But if you are doing
> differential expression analysis comparing the cell samples with the
> organ samples, you need to normalize
> all the samples together.
>
> --Naomi
>
> At 11:31 AM 11/1/2007, Bogdan Tanasa wrote:
> >Hi folks,
> >
> >I would like to ask for your opinions on the following:
> >
> >I have 60 expression profiles of 60 samples (cells and organs in
> >resting conditions).
> >I normalized these arrays in many ways, including RMA.
> >
> >Considering the biological arguments (cells samples vs organs
> >samples), I am planning to do the normalization separately, on the
> >group of cell samples, and on the group of organ samples.
> >
> >My questions are:
> >
> >- after RMA normalization on separate groups of samples (cells vs
> >organs), the results are different, but are these better ? GO analysis
> >do not display major differences.
> >
> >- would gcRMA work better than RMA ? The majority of opinions in SoCal
> >are pro-RMA.
> >
> >thanks,
> >
> >Bogdan
> >
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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
>

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