I'm running SAM in R package, I am analysing two affy array's groups data (two conditions in 3 separate pairs). I am using SAM starting from a filtered list containing 3000 genes but I had some problems. Infact when I analyze the delta table I have the number of the false positives that drastically goes down.For example, I have: Delta p0 False Called FDR 1 0.1 0.169 242.10 1259 0.033 2 0.2 0.169 31.10 272 0.019 3 0.4 0.169 2.50 23 0.018 4 0.5 0.169 1.10 13 0.014 5 0.7 0.169 0.15 3 0.008 6 0.8 0.169 0.15 3 0.008 7 1.0 0.169 0.10 2 0.008 8 1.1 0.169 0.05 1 0.008 9 1.3 0.169 0.05 1 0.008 10 1.4 0.169 0.05 1 0.008 anyone else has run across this and can tell me what should be done to solve it? Thanks mirella

lettieri@igb.cnr.it wrote: > > I'm running SAM in R package, I am analysing two affy array's groups data (two > conditions in 3 separate pairs). I am using SAM starting from a filtered list > containing 3000 genes but I had some problems. Infact when I analyze the delta > table I have the number of the false positives that drastically goes down.For > example, I have: > > Delta p0 False Called FDR > 1 0.1 0.169 242.10 1259 0.033 > 2 0.2 0.169 31.10 272 0.019 > 3 0.4 0.169 2.50 23 0.018 > 4 0.5 0.169 1.10 13 0.014 > 5 0.7 0.169 0.15 3 0.008 > 6 0.8 0.169 0.15 3 0.008 > 7 1.0 0.169 0.10 2 0.008 > 8 1.1 0.169 0.05 1 0.008 > 9 1.3 0.169 0.05 1 0.008 > 10 1.4 0.169 0.05 1 0.008 > > anyone else has run across this and can tell me what should be done to solve it? There are two problems here. If you are doing a paired analysis, there are only 2^3 permutations, so your null distribution will be very coarse. You would probably be better off using a t-distribution as your null rather than trying to permute (see the limma package). In addition, filtering your data down to 3000 genes that (I assume) are more likely to be differentially expressed is probably not a good idea. For a permutation method I would tend to use all genes and filter based on p-value and possibly fold change afterwards. Jim > > Thanks > > mirella > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623