[BioC] Different RMA expression values in different BioC versions?

[bmb at bmbolstad.com]

It would help if you could better quantify the exact size of the
differences ("very different" is somewhat open to interpretation). I don't
know if it is possible for you to reproduce this phenomenon again, but it
would be helpful to verify that it is a problem. Also if it is feasible
for you could you check the ReadAffy();rma() path just to ensure that it
is a justRMA problem rather than something to do with the internal C rma
code.
Best, Ben
> We have been using justRMA to generate RMA values for some time. Recently
> we
> noticed that the latest versions of R(2.4.0/2.4.1) together with BioC(1.9)
> gave very different RMA expression values. Just wondering if anybody else
> has
> the similar experience.
>
> Thank you very much in advance for your help!
> Quanli Wang
>