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eBayes with 1 biological replicate

Does anyone know why the error occurred when I just make a comparison of 1 time point (2hHGF) sample and 1 time point (2hnoHGF) sample? The error is shown in yellow below. And how to fix the error?

> samples<-as.factor(c("2hnoHGF","2hHGF","8noHGF","8hHGF","24noHGF","24hHGF"))
> design<-model.matrix(~0+samples)
> colnames(design)<-levels(samples)
> fit<-lmFit(selExpr,design)
> contrast.matrix<-makeContrasts(2hHGF-2hnoHGF, levels=design)
> fits<-contrasts.fit(fit,contrast.matrix)

> ebfit<-eBayes(fits)

Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  : 
  No residual degrees of freedom in linear model fits
r
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updated by Ram Ram • written by minni9234 • minni9234

1 answer

The conditions 2hHGF and 2hnoHGF have no replicates, so limma cannot estimate their dispersions. In other words, without replicates you can't tell whether an expression difference between 2hHGF and 2hnoHGF is due to the condition you want to test or it is due to the technical variability between arrays and samples.

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written by dariober dariober

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