[BioC] RMA with biological replicates
Dipl.-Ing. Johannes Rainer
johannes.rainer at tugraz.at
Thu Jul 29 15:22:27 CEST 2004
i have again a question about RMA and how it works with a different number of
we are looking at the response of patients to a specific treatment, so we got
biological replicates and no technical ones (as we have not enough material
from the patients). at the moment i got 9 chips, 3 patients, 3 time points for
What is now the best way to normalize them? normalize them all together with
RMA, or normalize the chips from each patient separatly (that means normalize
the 3 chips from patient one together, then those from patient 2...)?
As i think, RMA gives better results if i have more chips to normalize together
(more chips with roughly the same expression result in better fitted model
parameters i guess).
has anyone a conclusion what's the best was?
More information about the Bioconductor