Dear All,
I am having difficulty running Limma: every time I run the code R
crashes, and I can't explain the reason for the problem. Could someone
point me out to where to look for trouble? I attach the code and the error
messages below.
Thanks a lot in advance!
Olga
ERROR MESSAGE:
---------------
*** caught bus error ***
address 0x2c, cause 'invalid alignment'
Traceback:
1: sum(out$residuals^2)
2: lm.series(M, design = design, ndups = ndups, spacing = spacing,
weights = weights)
3: lmFit(eset, design)
4: NCOL(fit$coefficients)
5: contrasts.fit(lmFit(eset, design), contr.matrix)
6: ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim)
7: eBayes(contrasts.fit(lmFit(eset, design), contr.matrix))
CODE:
------
makeFit <- function(eset) {
design <- model.matrix(~0+factor(c(eset$stimulation)))
dimnames(design)[[2]] <- c("Control", "Insulin")
contr.matrix <- makeContrasts(Insulin-Control, levels=design)
eBayes( contrasts.fit( lmFit(eset, design), contr.matrix ) )
}
limmaFit <- makeFit(data$eset)
rm(makeFullFit)
SPECS:
--------
Mac OS X V.10.4.7, 1GHz PowerPC G4, 1.25GB memory
R Version 2.3.1 (2006-06-01)
> package.version("Biobase")
[1] "1.10.1"
> package.version("limma")
[1] "2.7.9"
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