[BioC] problem to compute copy number with crlmm

[Sören Gröttrup]

Hi,
I'm trying to compute the copy number for the Illumina 660W-Quad bead array
with the package crlmm. But for some chromosome it doesn't work and I get the
following message:

> computeCopynumber(crlmmSetList)
'batch' missing.  Assuming all samples in the CrlmmSetList object were
processed together in the same batch.
Fitting model for copy number estimation...
Using 50 df for inverse chi squares.
Sufficient statistics
.
Estimating coefficients
.Called from: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir =
envir)
Browse[1]>

What shall I do? When I press enter I get:

Error in nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir) :
  Inf values in W or V
> traceback()
5: stop("Inf values in W or V")
4: nuphiAllele(p = p, allele = "A", Ystar = YA, W = wA, envir = envir)
3: coefs(plateIndex = p, conf = conf[, plate == uplate[p]], envir = envir,
       CONF.THR = CONF.THR, MIN.OBS = MIN.OBS)
2: .computeCopynumber(chrom = CHR, A = A(ABset), B = B(ABset), calls =
calls(snpset),
       conf = confs(snpset), NP = A(NPset), plate = batch, envir = envir,
       SNR = ABset$SNR, bias.adj = FALSE, SNRmin = SNRmin, cdfName = cdfName,
       ...)
1: computeCopynumber(crlmmSetList)


What could be the problem? I'm glad for any help.

Thanks in advance
Sören