Is your method suitable for all microarray experiments, using both cDNA arrays and oligo arrays?
What I would say is that the good results that we have had reflect to some extent the kind of arrays that we print. As I said, we make nice big targets. If you print oligo arrays, for example, where the target is only a 70mer instead of a 1.5 kb species, then not all of the probes that you wind up labeling can bind to that small target, and consequently you would expect to see, and in fact do see, a good bit less signal. The method is certainly fine for use with other kinds of arrays like printed oligo arrays but won’t give you results that are comparable. In the paper, you compare your method against a conventional one. One explanation why you see such a large non-overlap when looking at two-fold over- or under-expression might be that the two methods favor different sets of genes. Why would that be? It’s a formal possibility. The conventional method is based on olig-dT priming and if the cDNA that you print represents the middle of the coding region as opposed to the 3’ non-coding re
