[BioC] Analyzing mulitple tissues

[Uri David Akavia]

Hello.

I had a run of chips, that included 3 kinds of tissues in different 
stages of differentiation. Only one repeat, due to budget and biological 
rarity reasons.

The tissues are
Cardiac1, Cardiac2, Cardiac3
Skeletal1, Skeletal2
MSC

My method of analysis is MAS 5.0, filtering (removing absent and lower 
than 20) and quantile normalization of the present genes.

I want to analyze the differentiation of Cardiac tissues, and the 
difference between MSC and Cardiac.

My question is - how should I filter and normalize the tissues? Should I 
filter and normalize just the tissues I want to analyze (which will give 
me different lists of genes for Cardiac/MSC and Skeletal/MSC) or should 
I filter and analyze all 6 samples, then only comparing the tissues I 
want (I'm afraid this will give me a lot of noise, with genes expressed 
at low levels)?
My problem with the first method is that it will be a different method 
for each set of tissues, even though I think it might be more accurate.

Thank you very much.

Yours,

Uri David Akavia