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