I am using siggenes to do a two class paired analysis of 36 microarrays. I do not appear to have any problems but upon summarizing the results I receive "NA" for fold change. I believe I read somewhere in the vingette that fold change is only calculated for two class unpaired analysis. Is this true? If not, what must I do in order to calculate the fold change in a two class paired analysis? Thanks, Mary University of California, San Diego > K<-18 > cl<-c((1:18),-1:-18) > mydata<- as .matrix (read.table("filter.txt",header=TRUE,sep="\t",row.names=1,as.is=TRUE)) > sam.out<-sam(mydata,cl,rand=123456) > sum.sam.out<-summary(sam.out,5.8) >sum.sam.out SAM Analysis for the Two-Class Paired Case s0 = 0 Number of permutations: 100 MEAN number of falsely called variables is computed. Delta: 5.8 cutlow: -7.086 cutup: 6.704 p0: 0.146 Identified Genes: 7988 Falsely Called Genes: 0 FDR: 0 Identified Genes (using Delta = 5.8): Row d.value stdev rawp q.value R.fold Name 1 15497 60.02 0.0715 0 0 NA 1439466_s_at 2 7512 52.20 0.0501 0 0 NA 1427036_a_at 3 11424 45.64 0.0501 0 0 NA 1433603_at 4 22076 42.52 0.0526 0 0 NA 1451019_at 5 24816 42.11 0.0720 0 0 NA 1455269_a_at 6 13851 40.63 0.0775 0 0 NA 1436983_at 7 15488 40.49 0.0757 0 0 NA 1439455_x_at 8 25290 40.40 0.0370 0 0 NA 1455975_x_at 9 6774 40.08 0.0814 0 0 NA 1426025_s_at 10 2060 39.92 0.0629 0 0 NA 1418594_a_at