Longitudinal data comparing a continuous variable in limma
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5.2 years ago
akknight • 0

Hi,

I'm new to limma and am trying to figure out how to test for differential expression using a continuous variable. My experimental set-up is two visits for each person and I want to look at change in expression between visit 1 and visit 2. However, I don't want to use visit 1 and visit 2 as the outcome as the visits were taken a various lengths of time apart, so I'm interested in modeling weeks post exposure (visit 1) verses weeks post exposure (visit 2). ( I want to see if there's an association with weeks) I've tried:

group<-pheno$Subject
cont.var<-pheno$Weeks
X<-splines::ns(cont.var,df=5)
design<-model.matrix(~0+group+X)
fit <- lmFit(edata2, design)
fit2<-eBayes(fit)
a<-topTable(fit2,coef="group", n=Inf, adjust="fdr")

(But this gives me output for each subject, not weeks)

Or

group<-pheno$Visit
cont.var<-pheno$Weeks
X<-splines::ns(cont.var,df=5)
design<-model.matrix(~group+X)
fit <- lmFit(edata2, design)
fit2<-eBayes(fit)
a<-topTable(fit2,coef="X5", n=Inf, adjust="fdr")

(But this seems equivalent to testing visit 1 verses visit 2) 

Unfortunately, I can't post the data here.

edata2 is a dataframe of log transformed expression values (Illumina platform)

Any ideas? 

 

limma timepoints longitudinal expression • 1.9k views
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