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

[James W. MacDonald]

Hi Stephen,

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? 

For the 100K chips, and assuming you are using the Affy software 
(GCOS/GDAS/GTYPE), you should be getting > 95% call rates. This is not 
possible for the 500K chips, so you have to adjust a setting - I believe 
it is the homozygote/heterozygote call thresholds - from 0.25 to 0.33 in 
order to get a call rate in the 90th percentile. This is why Affy has 
switched from using their maximum likelihood estimation method (they 
call DM) to BRLMM, which has a higher call rate for the larger chips.

CRLMM, which is implemented in the oligo package, probably has higher 
call rates than either of these two.

Note that the current implementation of oligo/makePlatformDesign 
requires _lots_ of RAM for even a small number of chips, so you will 
need at the very least a 64 bit OS and more RAM than I have (8 Gb).


Best,

Jim

> 
> 
> Stephen Henderson
> Wolfson Inst. for Biomedical Research
> Cruciform Bldg., Gower Street
> University College London
> United Kingdom, WC1E 6BT
> +44 (0)207 679 6827
> 
> 
> 
> 
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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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