[BioC] limma: duplicateCorrelation error

[Georg Otto]

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