Dear all,
I am analysing results from a spotted microarray with 9,600 features, spotted in duplicate. 
When I calculate the duplicate correlation, as follows:
 
	cor <- duplicateCorrelation(datanorm_ordered, design, ndups=2)

I get the following error message:
#5: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace = trace)

The consensus correlation coefficient is low (0.100) and also the distribution of correlation coefficients is between -0.1 and 0.5.

Still, I seem to get reasonable results from the model fit on the 8 arrays.
Does anyone know what the problem is here?

Thanks a lot,
Peter-Bram


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