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

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