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 TEL: 845-7313549 (o) 845-5486777 (h) ADD: 57 Old Forge Road, Tuxedo, NY, 10987 Dept. Environmental Medicine, School of Medicine New York University