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

[Benilton Carvalho]

What's the configuration you have available?

We're working on solutions to make it more memory efficient.

b

On Aug 17, 2006, at 9:25 AM, 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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