Question

crlmm package and allele-specific CNV with Illumina SNP arrays

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@zoppoli-gabriele-nihnci-g-4078

Last seen 10.2 years ago

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 at mail.nih.gov

SNP crlmm SNP crlmm • 1.1k views

ADD COMMENT • link updated 14.2 years ago by Rob Scharpf ▴ 250 • written 14.2 years ago by Zoppoli, Gabriele NIH/NCI [G] ▴ 20

score 0 · Answer 1 · 2010-10-04

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 [[alternative HTML version deleted]]