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"