[BioC] calculation of s0 (siggenes)

[Assa Yeroslaviz]

Hello,

IS there a way of calculating the s0-Value in the SAM analysis?
I did a few tets with my data. Every time I get the result
>data.sum
...
s0 = 0

 Number of permutations: 200

 MEAN number of falsely called genes is computed.

 Delta: 9.3
 cutlow: -23.092
 cutup: 14.528
 p0: 0.312
 Significant Genes: 8
 Falsely Called Genes: 0
 FDR: 0


Genes called significant (using Delta = 9.3):

    Row d.value stdev rawp q.value   R.fold      Name
1  4431    26.0  5.92    0       0 1.28e+42 254466_at
2 22511   -23.1 16.13    0       0 0.00e+00 259927_at
3  8199    18.4  5.61    0       0 1.83e+25 249456_at
4 14510    16.8  8.99    0       0 8.94e+40 258067_at
5  8351    16.4 10.68    0       0 3.08e+46 252077_at
6 16295    15.6  4.65    0       0 2.22e+20 263441_at
7  6168    14.9  7.62    0       0 1.35e+22 249015_at
8 22152    14.5 18.78    0       0      Inf 257088_at

I can define s0 as i like(in the sam line), but I'm not sure which value to
give.

THX,

Assa


--
Assa Yeroslaviz
Lötzenerstr. 15
51373 Leverkusen