I'm a student and I have doubts about how use Limma to contrast the differential gene expression evaluating my three variables: disease (case/control), gender(male/female) and age.
My data is like this: (three columns with the gender, age and the disease)
head(pData(gse))
Data Here:
I know build my experiment over my variable disease:
design= model.matrix(~ pData(gse)[,"disease"])
colnames(design)= c("control", "case")
fit= lmFit(gse, fesign)
fit1= eBayes(fit)
topTable(fit1, coef=2, adjust="BH", number= as.numeric(dim(gse)[1]))
But, How I can do a contrast Limma with my 3 variables? Thank for your help!
age= pData(gse)[,"age"]
gender= pData(gse)[,"gender"]
disease= pData(gse)[,"disease"]
age.group= ifelse(age>40,"over40", "under40")
design = model.matrix(~0 + disease + gender + gender:age)
contr.matrix <- makeContrasts( **???**