[BioC] very small fold change from RMA data

[Dapeng Cui]

Hi,

My question is about very small fold change from RMA treated data. What I did is to normalize affy chips with RMA, transform to linear values then import to GeneSpring. Data was filtered using Affy detection call.  Then a two group T-Test (10 replicates in each conditions) was performed and gave me a list of 300 gens.  What makes me confused is that 50% of these genes have fold changes less than 1.2, only 10% genes have higher than 1.5 fold change.  Is this normal? 

I also did the same T-Test with Affy pre-scaled data (and nomarlized with GeneSpring per chip and per gene median normalization). This time 50% of genes in the list have higher than 1.5 fold changes. (And this list is not the same as that one from RMA data, only 70% overlapping.) 

I will appreciate it very much if anybody could provide me some literature regarding different normarlizations and fold change. Thanks. 

dapeng cui