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

Hi Dapeng Cui, there is a trade-off between variance and bias when estimating fold-change, esp. for weakly expressed genes. "Bias" means that the estimated fold-changes for genes whose true fold-changes are different from 1 are shrunken towards 1. While the MAS-software stays on the high-variance, small-bias side, RMA tends to sacrifice some bias for a large gain in variance. Thus, the fold-changes from RMA will often be closer to 1 than those from MAS, esp. for weakly expressed genes. Best regards ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Thu, 16 Oct 2003, Dapeng Cui wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >