[BioC] Affymetrix 500k SNP chips -- copy number/LOH/deletions

[Stephen Henderson]

Is there software for analysing copy number/LOH/deletions in SNP data
using R/Bioconductor?

Plus apologies for being slightly off-topic but

Does anyone know what typical Call rates are for a good analysis of 500k
SNP chips? I have calls from about 87-95%, and have heard that 93% is
good for 100k chips. Is this range acceptable/ usual for 500k chips? 


Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827




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