[BioC] Inf values using SAM (package=siggenes)

[Julian Lee]

Dear All,

I'm having some problems trying to find differentially expressed genes using SAM. I have the SAM for excel version but that unfortunately is limited to only 500 genes.

from the vignette, i'm supplying the sam function, two important arguments, data and cl.

> data
ExpressionSet (storageMode: lockedEnvironment)
assayData: 16304 features, 65 samples 
  element names: exprs 
phenoData
  rowNames: D02_2nd, D02_3rd, ..., D31_BL (65 total)
  varLabels and varMetadata:
    Patient_ID: Patient's ID
    Patient_Initials: Patient's Initials
    ...: ...
    25_at_cycle1: 25% reduction from baseline at cycle1
    (17 total)
featureData
  rowNames: 1007_s_at, 1053_at, ..., AFFX-r2-Ec-bioD-5_at (16304 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "hgu133plus2"

>cl
[1] 1 1 0 1 1 0 1 1 0 1 0 1 1 1 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 1 0 1 1 0 1 1
[39] 1 1 0 1 1 0 1 1 0 1 1 1 0 1 0 1 1 0 1 1 0 1 0 1 0 1 0

data was pre-processed using the rma function, followed by genefiltering

>data<-rma(U133PLUS2 CELFILES)
>library(genefilter)
>f1<-pOverA(0.25,log2(100))
>f2<-function(x) (IQR(x)>0.5)
>ff<-filterfun(f1,f2)
>data<-data[genefilter(data,ff),]

##56,000 genes reduced to 16304 genes

>library(siggenes)

>sam.out<-sam(exprs(data),cl,rand=1234)
>sam.out
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances 
 
   Delta p0 False Called FDR
1    0.1  1     0      0   0
2    0.2  1     0      0   0
3    0.3  1     0      0   0
4    0.4  1     0      0   0
5    0.5  1     0      0   0
6    0.6  1     0      0   0
7    0.7  1     0      0   0
8    0.8  1     0      0   0
9    0.9  1     0      0   0
10   1.0  1     0      0   0

>summary(sam.out)
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances 
 
 s0 = 0.0735  (The 0 % quantile of the s values.) 
 
 Number of permutations: 100  

 MEAN number of falsely called variables is computed.

   Delta p0 False Called FDR cutlow cutup j2    j1
1    0.1  1     0      0   0   -Inf   Inf  0 16305
2    0.2  1     0      0   0   -Inf   Inf  0 16305
3    0.3  1     0      0   0   -Inf   Inf  0 16305
4    0.4  1     0      0   0   -Inf   Inf  0 16305
5    0.5  1     0      0   0   -Inf   Inf  0 16305
6    0.6  1     0      0   0   -Inf   Inf  0 16305
7    0.7  1     0      0   0   -Inf   Inf  0 16305
8    0.8  1     0      0   0   -Inf   Inf  0 16305
9    0.9  1     0      0   0   -Inf   Inf  0 16305
10   1.0  1     0      0   0   -Inf   Inf  0 16305

I'm not too sure why i'm getting Infinity values. This is my first time using SAM on bioconductor. 

Thank you

regards

Julian Lee
National Cancer Center Singapore

>sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "methods"   "base"     

other attached packages:
genefilter       maDB      limma       affy     affyio   siggenes   multtest 
  "1.14.1"    "1.8.0"   "2.10.5"   "1.14.2"    "1.4.1"   "1.10.1"   "1.16.1" 
  survival    Biobase 
    "2.32"   "1.14.1"