[BioC] GCRMA backgrounds?

Zhijin Wu zwu at jhsph.edu
Wed Jul 21 23:14:58 CEST 2004

There is some changes between the older version and the newer ones. The
original use of sequence information only considered GC counts in the
probe sequence, while later a more sophisticated model is used that
considers the position and types of base. This difference comes from our
approach on using the sequence information, not from the speed.


On Wed, 21 Jul 2004, Andrew Harrison wrote:

> Hi,
> 	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,
> 		Harry
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

More information about the Bioconductor mailing list