search for: gquantil

...>>what is down-regulated looks down-regulated. The difference is that the >>down-regulated (and not in the up), so so much more down-regulated in one >>of the batches. It looks like to be that the universal has more mRNA >>abundance in one batch over the other. > >Gquantile won't help because it doesn't change the M-values. (It is >intended for use with single channel analyses.) You could try 'quantile' >or 'scale' normalization (not both) but there are no magic bullets in a >situation like this. If you use 'scale normalization...