[BioC] problem to compute copy number with crlmm

[Sören Gröttrup]

I'm sorry. Here my sessionInfo():

> sessionInfo()
R version 2.10.0 RC (2009-10-18 r50160)
x86_64-pc-linux-gnu

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] human660quadv1aCrlmm_1.0.0 crlmm_1.4.0
[3] Biobase_2.6.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.8.0  Biostrings_2.14.0    DBI_0.2-4
 [4] IRanges_1.4.0        RSQLite_0.7-3        SNPchip_1.10.0
 [7] affyio_1.14.0        annotate_1.24.0      ellipse_0.3-5
[10] genefilter_1.28.0    mvtnorm_0.9-8        oligoClasses_1.8.0
[13] preprocessCore_1.8.0 splines_2.10.0       survival_2.35-7
[16] tools_2.10.0         xtable_1.5-5




Vincent Carey schrieb am 2009-11-11:
> be sure to send your sessionInfo() output to help with diagnosis

> On Wed, Nov 11, 2009 at 5:40 AM, Sören Gröttrup
> <soerengroettrup at uni-muenster.de> wrote:
> > 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

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