[BioC] quantile normalization

[Martino Barenco]

Hi,

My understanding of quantile normalization is that values for several 
data sets are ranked, then the average per rank is taken and is 
reattributed to each data set according to the original rank (hope this 
makes sense). My question is: how does one deal when ties occur?
- One possibility would be to force a tied value to be greater than the 
other (using the "order" command instead of "rank"). Even though it 
would not make a huge difference it is a bit arbitrary.
- Another possibility is to "force" the ties across all data sets, 
quite arbitrary as well.
- or maybe a combination of both, but it looks like a nightmare to 
program!

So, what should be done? Also, is there a method such as "normalize" 
that acts on exprSet rather than AffyBatch?

Thanks

Martino
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Martino Barenco
CoMPLEX
4, Stephenson Way
London NW1 2HE
Tel.: +44 20 7679 5088
Fax.: +44 20 7383 5519
Email: m.barenco at ucl.ac.uk