Message-ID: <1114009117.42666e1d5e2bd@mail.igb.cnr.it>
Date: 2005-04-20T14:58:37Z
From: lettieri@igb.cnr.it
Subject: sam analysis question
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