crlmm package and allele-specific CNV with Illumina SNP arrays
1
0
Entering edit mode
@zoppoli-gabriele-nihnci-g-4078
Last seen 9.7 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
0
Entering edit mode
Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 9.7 years ago
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]]
ADD COMMENT

Login before adding your answer.

Traffic: 778 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6