[BioC] problem to compute copy number with crlmm

[Sören Gröttrup]

Thanks for the fast answer. I will install the new version as soon as
possible.

I have 12 samples available. But some of them contain the same data because I
copied them to get more then 10 samples. Hope that's not a problem.

Sören


Benilton Carvalho schrieb am 2009-11-11:
> Dear Soren,

> apologies for the inconvenience.

> I have fixed the problem and just uploaded a new version of the
> crlmm  package to address this issua (version 1.4.1), which should
> be  available in 1 (max 2) days.

> This fixes the "Browse[1]>" thing you saw. Now , regarding the error
>  "Inf values in W or V", how many samples do you have available?

> Thanks a lot,

> b

> On Nov 11, 2009, at 9:31 AM, Sören Gröttrup wrote:

> >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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