[BioC] crlmm package and allele-specific CNV with Illumina SNP arrays

Zoppoli, Gabriele (NIH/NCI) [G] zoppolig at mail.nih.gov
Sun Oct 3 19:25:39 CEST 2010

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)

[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

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