Hi, > path1 <- kegg[["00280"]]; > globaltest_all <- globaltest(esetSub2,pData(esetSub2)[,"scanner2"],test.genes = path1,model = "logistic"); > geneplot(globaltest_all,labelsize = 1); here, it shows only 1 gene(145512_at) out of my all 6 samples. I have 3 Knock Out and 3 Wild Type samples. > sampleplot(globaltest_all,labelsize = 1); here, I can see all 6 sample plots look similar , Knock out and Wild Type. Very less difference. I think , it should only show Knock out sample at higher bar..right..! Am I doing something wrong or I have wrong undertanding..about sampleplot and geneplots. (or Need to read more about that) Please let me know..if anyone..! Thanks, Saurin