[BioC] 100K SNP chips for linkage

[James W. MacDonald]

Justine Peeters wrote:
> Hello,
> 
> I was wondering if there were any R packages as yet for analysing 100K Affy
> SNP chips specifically for linkage/autozygosity? Is there anyone who has
> experience in analysing 100K SNP chips?

Not yet, but we are working on it. The existing infrastructure for 
handling raw Affy data are not amenable to the new SNP chips, so we need 
both a package to handle the raw data as well as a package with the 
methods to analyze.

We are still in the preliminary stages, but hopefully will have 
something useful this Summer. In the interim, Affy's GCOS will do the 
linkage and SNP calls, and they also have a copy number tool if you are 
interested in additions/deletions.

Best,

Jim



> 
> Regards, Justine
> 
>  
> 
> Justine Peeters
> 
> Bioinformatician
> 
>  
> 
> Department of Bioinformatics
> 
> ErasmusMC
> 
> Postbus 1738, 3000DR 
> 
> Rotterdam, Netherlands
> 
> Kamer Ee15.38a
> 
>  
> 
> +31 624668045
> 
>  
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623