[BioC] SAM output in siggenes package

[Anna Cao]

Hi,

I recently perform SAM using the siggenes package. I'm doing SAM on
untreated vs untreated cultured for 1 hour sample. I have 16 replicates and
am doing the paired two-class SAM. Ideally, there should be no significant
genes but SAM in R gave me a lot of significant genes (~6000 genes with ~0%
FDR). I counted the number of 2 fold genes and they are less than 100. Are
there any parameters that I missed and need to adjust b/c this result seems
incorrect.

Here's my input and output:
> sam.UT60<-sam(RG.UT60, x=c(1:16),y=c(17:32),paired=TRUE,B=200,na.rm=TRUE)
Warning: There are 7958 genes with at least one missing value.
 
s0 = 0 
 
SAM Analysis for a set of delta: 
   delta    p0   false called   FDR
1    0.2 0.245 10801.0  13948 0.189
2    0.4 0.245  8877.0  13385 0.162
3    0.6 0.245  6079.5  12508 0.119
4    0.8 0.245  3797.0  11577 0.080
5    1.0 0.245  1704.0   9837 0.042
6    1.2 0.245   812.0   8630 0.023
7    1.4 0.245   391.0   7671 0.012
8    1.6 0.245   182.5   6846 0.007
9    1.8 0.245    85.0   6091 0.003
10   2.0 0.245    39.0   5312 0.002

Warning messages: 
1: multi-argument returns are deprecated in: return(r, s, r.perm, s.perm, Z,
mat.samp, var.0.genes, NA.genes) 
2: multi-argument returns are deprecated in: return(alpha.hat, s.zero, cv,
cv.zero) 
3: multi-argument returns are deprecated in: return(p0, spline.out, vec.p0) 
4: multi-argument returns are deprecated in: return(tab.fdr, mat.fdr, p0) 
5: multi-argument returns are deprecated in: return(d, d.sort, s, d.bar,
d.perm, mat.samp, s0, FDR, p0, fdr.ngenes,  

BTW, why am I getting these warning messages?

THANKS! 

Anna