[BioC] normalization question

[Phguardiol@aol.com]

Hi all,
I am pretty new in this list so I hope my question is not going to be 
"inappropriate" for it ! Here is my problem:
I have one human cell line Cw that is diploid and has a deficient gene FA, 
this cell line has been corrected for this deficient gene (name is Cneo), and 
I have also another cell line that evolved from Cw with 95% of cells being 
now tetraploid (and FA deficient, name Ctetra). I d like to compare this new 
tetraploid cell line to the 2 others. Besides, I have duplicates - and soon 
triplicates - for these in 2 different conditions applied to all these cells: 
normal culture conditions or incubation with a drug. I am using Affy HG 
U133A/B chips. I was wondering what kind of normalization I should use for a 
comparison such as Cw versus Ctetra without any drug ? Should I normalize all 
my diploid chips and then separately normalize all my tetraploid chips then 
pool them for analysis ? or can I normalize all the chips in the same process 
? Then do my comparisons 
Thanks for your help
Philippe Guardiola, MD 

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