From an email from johnq:
One of the things that has bothered me over the years in MeV has been the PCA which can produce somewhat skewed results for non-centered data.
I would like to add an option (which should be selected by default) for PCA.
If one does PCA on genes, the experiments should be median centered before initiating the calculation. We should not median center the data in the way that selecting the median center transformation does, but we should do it within PCA. Users should have the option of choosing median center (default), mean center, or none (radio buttons come to mind).
For PCA on samples, the options should apply to the genes.
This should be a relatively simple patch, but it would be nice to have.