[BioC] problem to compute copy number with crlmm

[Benilton Carvalho]

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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