Question: eBayes with 1 biological replicate
0
gravatar for minni9234
5.4 years ago by
minni923450
United States
minni923450 wrote:

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 • 1.9k views
ADD COMMENTlink modified 5.4 years ago by dariober10k • written 5.4 years ago by minni923450
4
gravatar for dariober
5.4 years ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:

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.

ADD COMMENTlink written 5.4 years ago by dariober10k
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