Dear Bioconductors, I am working with an array containing 17496 probes spotted in duplicate. To deal with duplicate spots I used duplicateCorrelation like this: cor<-duplicateCorrelation(MA,ndups=2, spacing=1458) This results in a warning message: Warning message: Too much damping - convergence tolerance not achievable in: glmgam.fit(dx, dy, s tart = start, tol = tol, maxit = maxit, trace = trace) Despite this, I get a result out of it: cor$consensus.correlation [1] 0.60528 which i use like this: fit<-lmFit(MA, ndups=2, correlation=0.60528) fit<-ebayes(fit) writing the M values from fit to a table, I notice that some probes are missing from the output. I looked at differences to a fit that was done without duplicateCorrelation trying to rule out that there is a problem with the spacing of probes. I looked at three consecutive probes that are duplicated with the same spacing, but after duplicateCorrelation the middle one is missing while the two other ones are there in duplicates. This leaves me clueless... Any idea? Best, Georg -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49-7071-601 301 http://www.eb.tuebingen.mpg.de

> Date: Fri, 18 Feb 2005 13:20:00 +0100 > From: Georg Otto <georg.otto@tuebingen.mpg.de> > Subject: [BioC] limma: duplicateCorrelation error > To: bioconductor@stat.math.ethz.ch > > Dear Bioconductors, > > I am working with an array containing 17496 probes spotted in > duplicate. To deal with duplicate spots I used duplicateCorrelation > like this: > > cor<-duplicateCorrelation(MA,ndups=2, spacing=1458) > > This results in a warning message: > > Warning message: > Too much damping - convergence tolerance not achievable in: > glmgam.fit(dx, dy, s > tart = start, tol = tol, maxit = maxit, trace = trace) > > Despite this, I get a result out of it: > > cor$consensus.correlation > [1] 0.60528 > > which i use like this: > > fit<-lmFit(MA, ndups=2, correlation=0.60528) > fit<-ebayes(fit) There are warnings and there are errors. This is not an error as you've said in the subject line, it is a warning. This question has been asked quite a few times on this list. As I've said each time, it is not a problem. duplicateCorrelation() take the consensus of a large number of correlations, and it makes virtually no difference that one correlation out of thousands could not be computed. Gordon > writing the M values from fit to a table, I notice that some probes are > missing from the output. I looked at differences to a fit that was done > without duplicateCorrelation trying to rule out that there is a problem > with the spacing of probes. I looked at three consecutive probes that > are duplicated with the same spacing, but after duplicateCorrelation > the middle one is missing while the two other ones are there in > duplicates. This leaves me clueless... > > Any idea? > > Best, > > Georg > > -- > Georg Wilhelm Otto > Max-Planck-Institute for Developmental Biology > Spemannstrasse 35/III > D-72076 Tuebingen Germany > phone: +49-7071-601 301 > http://www.eb.tuebingen.mpg.de