Hi Gabriele,

The pdf of the vignette is correctly rendered in crlmm v 1.6.6.  Or you can find the file illumina_copynumber.Rnw in crlmm/inst/scripts.  The script starts from the *.idat files.

Rob
On Oct 4, 2010, at 6:00 AM, bioconductor-request@stat.math.ethz.ch wrote:

> Message: 1
> Date: Sun, 3 Oct 2010 13:25:39 -0400
> From: "Zoppoli, Gabriele (NIH/NCI) [G]" <zoppolig@mail.nih.gov>
> To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
> Subject: [BioC] crlmm package and allele-specific CNV with Illumina
>        SNP     arrays
> Message-ID:
>        <1B47D0B4AB919F4893D52BE2F1E3165A22E92142F9@NIHMLBX11.nih.gov>
> Content-Type: text/plain; charset="us-ascii"
> 
> Here is the information on my R session:
> Dear Bioconductor mailing list,
> 
> is there a vignette or an explanation somewhere, or can anybody tell me how to perform allele-specific CNV with the package crlmm and Illumina SNP arrays? My issue is that I only have the *.idat files!
> 
> Here is the information on my Bioc session, thanks to everybody in advance!
> 
> 
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] human1mv1cCrlmm_1.0.1 crlmm_1.6.5           oligoClasses_1.10.0
> [4] Biobase_2.8.0
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.10.2  Biostrings_2.16.9     DBI_0.2-5
> [4] IRanges_1.6.14        RSQLite_0.9-2         affyio_1.16.0
> [7] annotate_1.26.1       bit_1.1-4             ellipse_0.3-5
> [10] ff_2.1-2              genefilter_1.30.0     mvtnorm_0.9-92
> [13] preprocessCore_1.10.0 splines_2.11.1        survival_2.35-8
> [16] tools_2.11.1          xtable_1.5-6
> 
> 
> 
> Gabriele Zoppoli, MD
> Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy
> Guest Researcher, LMP, NCI, NIH, Bethesda MD
> 
> Work: 301-451-8575
> Mobile: 301-204-5642
> Email: zoppolig@mail.nih.gov


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