[BioC] Siggenes output only gives NAs?

[Tiago R Magalhaes]

Hi

I am using R 2.0.1 in a MacOs 10.3.7.

I am using Siggenes to do SAM analysis. I want to get the genes that 
are differentially between WT and Cond1, using the two class unpaired 
data.

I have run into this problem where some of my analysis yield only 
NAs. I have looked in the archives, and there's some mention to this 
but in previous version of Siggenes. Did anyone had the same problem 
with the most recent version of Siggenes?

Here is a basic description of my data: 1 case where everything is 
ok, the other where I only get NAs. I can send more detailed 
information if needed.

Thanks for any help.

1) case where everthing went fine
argument data for sam:
    data.frame:	14010 obs. of  9 variables:
    WT.a  : num   10.3  95.6 469.7 416.0 536.3 ...
    WT.b  : num   14  50 917 658 775 ...
    WT.c  : num   50.3  56.5 809.5 525.8 729.4 ...
    WT.d  : num    73.6   15.8  829.7  664.4 1218.0 ...
    WT.e  : num   20.8  25.7 963.2 800.6 836.4 ...

    Cond1.a: num   20.7  23.6 706.1 568.8 706.3 ...
    Cond1.b: num   66.0  39.7 842.1 667.5 719.3 ...
    Cond1.c: num   72.1  51.9 896.5 737.2 868.7 ...
    Cond1.d: num   28.1  64.8 489.5 607.5 835.0 ...

output of sam (slot d)
   d.statistic: num   0.724 -0.226 -0.513  0.430 -0.308 ...

2) case where I only get NAs
argument data for sam:
   WT.a  : num   605 4467 1554 1896 2591 ...
   WT.b  : num  1123 3486 2828 2586 3117 ...
   WT.c  : num  1216 3633 2948 2351 2654 ...
   WT.d  : num  1272 3577 3088 2276 2674 ...
   WT.e  : num  1203 3905 2424 2362 2365 ...

   Cond2.a: num  1174 2727 2651 1660 2672 ...
   Cond2.b: num  1173 2425 2512 1512 2361 ...
   Cond3.c: num  1142 2843 2443 1552 2423 ...
   Cond4.d: num  1139 3579 2566 1449 2649 ...

output of sam (slot d)
     d.statistic: num [1:14010] NA NA NA NA NA NA NA NA NA NA ...