ArrayExpress dataset of 5 individuals 2 different tissues: "V" and "A". I want to compare the gene differential expression of "V" and "A" as paired sample for each individual.

I have used this code so far.

library(ArrayExpress) library(limma) rawdata=ArrayExpress("E-blablabla") eset<-rma(rawdata) Patients<-factor(rep(1:5,2)) Tissues<-factor(c(rep("V",5),rep("A",5))) design<-model.matrix(~Patients+Tissues) fit<-lmFit(eset,design) fit<-eBayes(fit)

According to limma User's Guide i should continue with

topTable(fit,coef=??)

What should coef be? I do not understand their example in the User's Guide (coef="TreatT").

If I type

colnames(design)

I get

[1] "(Intercept)" "Patients2" "Patients3" [4] "Patients4" "Patients5" "TissuesV

Coefficient should correspond to what exacly?

Also, how do I write to file for easier interpretation?

Thanks

Thanks for the help!