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

[James W. MacDonald]

dChipSNP might be more memory friendly.

Stephen Henderson wrote:
> 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 at 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 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
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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