[BioC] GCRMA backgrounds?

Andrew Harrison harry at biochemistry.ucl.ac.uk
Wed Jul 21 16:43:51 CEST 2004


	I've been using GCRMA and the new speedier version (1.1) 
gives different values than the older slower version (1.0). 

	Looking through the bioconductor mails suggests that 
a few other people identified a similar problem, related to a
background not being subtracted. Hopefully people are on the case, 
but this problem seems to have been around since April. I've been 
plugging GCRMA to my colleagues, who are now starting to use it, 
so I hope the problem can be sorted out.

	On a different note, what technical limitations stop 
Affymetrix going for much longer probes than 25 bases? The work 
of Naef and Magnasco, and Wu and Irizarry, highlight the 
limitations of Affy technology due to cross-hybridisation, when 
there are only 25 bases. Pushing upwards to 50 bases will reduce CH, 
but what other factors then come in? 

	My understanding is that the Affy SNP chips have 25 base 
oligos. What is stopping these chips from also having 
cross-hybridisation issues?	

	Best wishes,

Dr Andrew Harrison                               Tel: 44 (0) 207 679 3890   
Biomolecular Structure and Modelling Unit        Fax: 44 (0) 207 679 7193
Biochemistry and Molecular Biology Dept.     
University College London
Gower Street                       	   Email: harry at biochem.ucl.ac.uk
London, WC1E 6BT, UK                  http://www.biochem.ucl.ac.uk/~harry

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