[BioC] very small fold change from RMA data

[Qiang Li]

Hi, Dapeng,

I noticed your question about very small fold change in RMA data by 
GeneSpring. I encountered same problem right now. I was wondering whether 
you found out the solution or answer. Thanks

Best regards

Qiang Li


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

Qiang Li

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