[BioC] Limma error

[James MacDonald]

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

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "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",
"group5")
> 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



   Thanks 

   Amin Momin

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