[BioC] very small fold change from RMA data
bioddc at langate.gsu.edu
Thu Oct 16 17:15:14 MEST 2003
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.
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