[BioC] Limma error

James MacDonald jmacdon at med.umich.edu
Fri Nov 21 16:27:13 MET 2003

There was a bug in limma that kept it from using an exprSet correctly.
The development version contains the fixed version of lmFit.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Amin Momin" <gtg269c at mail.gatech.edu> 11/21/03 10:00AM >>>
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 =
        No residual degrees of freedom in linear model fits


   Amin Momin

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