[BioC] Cancer genome project SNP data

[Daniel Brewer]

Hi,

I am trying to replicate the results gained from the Affymetrix SNP 10K
experiments in the cancer genome project
(http://www.sanger.ac.uk/genetics/CGP/).  The publicly accessible data
files (ftp://ftp.sanger.ac.uk/pub/CGP/affy/) are found in this format:
SNP_NUMBER	SNP_NAME	PMS	MMS	PMA	MMA
1	SNP_A-1513509	5901.9	3925.3	3815.1	2648.4
2	SNP_A-1513556	6280.3	5403.5	7412.3	5743.5
3	SNP_A-1518411	7047.3	3734.9	4357.4	2315.6

where according to the README:
SNP_NUMBER	= Affymetrix internally assigned reference number
SNP_NAME	= Affymertix SNP identifier
PMS	= Perfect match (sense) intensity value
MMS	= Mismatch (sense) intensity value
PMA	= Perfect match (antisense) intensity value
MMA	= Mismatch (antisense) intensity value

Does anyone have any idea on how I can get the copy number from this data?

Tried all the possible ratios but they do not seem to produce accurate
results.

Daniel Brewer
-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109
Fax: +44 (0) 20 8722 4141

Email: daniel.brewer at icr.ac.uk