[BioC] OT: random priming labelling - label nucleotide or primer?

[J.delasHeras at ed.ac.uk]

This is not really bioconductor, as it relates to sample labelling...  
but if the labelling works then I'll have data to analyse with BioC,  
so I hope you forgive me being off-topic this time ;-)

The question:

We've used a random priming method to label our genomic DNA samples  
for microarray analysis.
We use random primers (unlabelled) and incorporate labelled dCTP (Cy3  
or Cy5) with Klenow.

Now, we're going to start hybridising ourselves arrays from Nimblegen,  
and their method uses labelled random 9-mers, and non-labelled dNTPs:  
the opposite approach.

Does anybody have any preference of one method over another?

Using labelled oligos according to Nimblegen's protocol is over 3x  
cheaper than the method we're currently using. On the other hand, our  
method works well in our hands! So you see my dilemma... changing  
something that works in order to make some savings...

Any comments appreciated!

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK