[BioC] RMA vs gcRMA on 2 groups of samples

[Naomi Altman]

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)
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