[BioC] justGCRMA normalisation options?

[Andrew Harrison]

Hi,

	Firstly, GCRMA rocks and many thanks to all those 
involved in producing it. 

	However, GCRMA is painfully slow. I understand there are plans 
for a justGCRMA. Will the fast version have options for normalisation 
other than the default quantiles? QN is good for merging replicates, 
which should all have the same distribution. However, it introduces 
artifacts when comparing chips from different conditions which are 
observed to have different distributions.

	Is it possible to have a quick version for just the 
background calculation? And possibly another quick version for 
the median polish expression summary? But I think the normalisation 
choice should not be hardcoded.

	Or is this heresy?

	Thanks again,
		Harry

-- 
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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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