[BioC] Analyzing mulitple tissues

[Uri David Akavia]

Gordon Smyth wrote:
> There isn't any conflict between Naomi's comments and my own. Naomi 
> actually refered to "biological replication" rather than to replication 
> per se. She was reacting to Uri's original post which made it very 
> unclear whether there is any biological replication in his experiment at 
> all, i.e., it may be that Cardiac1, Cardiac2 etc are not in fact 
> biological replicates. Replication is a subtle business, and Uri would 
> need to describe his process and population in much more detail than he 
> done for more to be said. I may be wrong, but I doubt that Naomi was 
> especially concerned about the single MSC chip.

Actually, you're correct.
Cardiac1, Cardiac2 are different stages of the same tissue.
They are NOT biological replicates.

However, I think my question was misunderstood.
I use quantile normalization and select genes by fold change.

I wish to see the differentiation of Cardiac, and to compare Cardiac to MSC.
My question is: Should I normalize on all tissues, or simply on the 
tissues analyzed at the time?
If I normalize all 6 samples, I'm afraid that the smaller differences 
between Cardiac will be masked by the larger differences between Cardiac 
and MSC.
If I normalize only the tissues analyzed, it means that I will normalize 
multiple times, each time differently for different tissue (leading to 
different values).

What is preferable? What are additional pros and cons for each method?

Thank you,

Uri David Akavia