>Date: Thu, 22 Sep 2005 07:38:19 +0200 >From: "Hoen, P.A.C. 't \(HKG\)" <p.a.c._t_hoen at="" lumc.nl=""> >Subject: [BioC] LIMMA: duplicate correlation >To: <bioconductor at="" stat.math.ethz.ch=""> > >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) This is not an error message, this is a WARNING. As I have said many times on this list, getting a small number of warning messages from duplicateCorrelation() is not a problem. Ignore it. Gordon >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