[BioC] Limma error

Amin Momin gtg269c at mail.gatech.edu
Fri Nov 21 16:00:29 MET 2003

Hi ,

    I have been trying to use limma to construct linear model of my
normalized affymetrix data, but the program gives me an error at the
last step of the calculation by empirical bayes. Can someone using the
package give a comment on my error.

> design <- model.matrix(~ -1+factor(c(1,2,3,4,5,1,2,3,4,5)))
> colnames(design) <- c("group1", "group2", "group3", "group4",
> fit <- lmFit(esetsarco, design)
> contrast.matrix <- makeContrasts(group1-group2, group1-group3,
group1-group4, group1-group5, group2-group3, group2-group4,
group2-group5, group3-group4, group3-group5, levels=design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
Error in ebayes(fit = fit, proportion = proportion, std.coef = std.coef)
        No residual degrees of freedom in linear model fits


   Amin Momin

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