Hi. I am trying to analyse a dataset which has 2 different stress (drought and pathogen on arabidopsis). I have downloaded three different experiments from GEO for each of the stresses. I am trying to analyse different experiments separately and then pick put the common genes between both the stresses. I am new to R bioconductor. My script upto toptable works just fine. But I doubt the script after that. Please check the script below >result=decideTests(fit2, lfc=1) >drought.genes=names(which(result[,"D.Exp1"]!=0 & result[,"D.Exp2"]!=0 & result[,"D.Exp3"]!=0)) >pathogen.genes=names(which(result[,"P.Exp1"]!=0 & result[,"P.Exp2"]!=0 & result[,"P.Exp3"]!=0)) Here drought.genes gives me a list of >450 genes but pathogen.genes gives me only 4 genes Please help. -- *Chirag Gupta* Department of Crop, Soil, and Environmental Sciences, 115 Plant Sciences Building, Fayetteville, Arkansas 72701 [[alternative HTML version deleted]]