trouble running Bioconductor
Hmm, in case you installed Bioconductor from source, did you remember to install the version of GCC that ships with the CRAN version of R? That, or some other installation mishap is all I can think of. Kasper
On Aug 10, 2006, at 6:33 PM, Olga Vitek wrote:
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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