That call rate is from Affymetrix own GTYPE software.

I did not run the analysis but I believe that the NoCall threshold is below 0.33 confidence.

I have tried Beniltons software but sadly found I did not not have enough memory.

-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: Thu 8/17/2006 1:41 PM
To: Stephen Henderson; Bioconductor
Subject: Re: [BioC] Affymetrix 500k SNP chips -- copy number/LOH/deletions
 



On 8/17/06 8:36 AM, "Stephen Henderson" <s.henderson@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



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