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

[Benilton Carvalho]

Hi Stephen,

the oligo package

http://www.bioconductor.org/packages/1.9/bioc/

provides tools for dealing with the SNP arrays. We do not have  
anything ready for CNA as for now, but you can start exploring your  
data.

You will need also the Platform Design Environments available at:

http://www.biostat.jhsph.edu/~bcarvalh/research.html

Please, let me know if you need anything else.

b

On Aug 17, 2006, at 8:36 AM, Stephen Henderson wrote:

> Is there software for analysing copy number/LOH/deletions in SNP data
> using R/Bioconductor?
>
> 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?
>
>
> Stephen Henderson
> Wolfson Inst. for Biomedical Research
> Cruciform Bldg., Gower Street
> University College London
> United Kingdom, WC1E 6BT
> +44 (0)207 679 6827