Hi Everybody,

I have four columns of log2-transformed ratio data (http://ifile.it/ija65rq).
I want to analyze it with LIMMA, but stuck with duplicateCorrelation:

> library(limma)
> M <- read.delim('M.txt')
> design <- cbind(c(-1, 0, -1, 0), c(0, -1, 0, -1))
> corr <- duplicateCorrelation(M, design=design, spacing=5776, ndups=3)
Error in glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
trace) :
        Starting values give negative fitted values

Does anybody has similar experience and any hints to share?

Thanks very much,

York

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