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

[Sean Davis]

On 8/17/06 8:36 AM, "Stephen Henderson" <s.henderson at ucl.ac.uk> wrote:

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

Benilton will probably reply directly, but you might look at the oligo
package.

> 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?

What allele-calling software are you using that is giving those rates?

Sean