[BioC] sam analysis question

[lettieri at igb.cnr.it]

 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