[BioC] RMA with biological replicates

[James MacDonald]

You will want to run rma on all the chips together. There are not very
many instances where it makes sense to run rma on separate batches of
chips and then try to combine them.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 07/29/04
09:22AM >>>
hi,

i have again a question about RMA and how it works with a different
number of
chips.
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
each patient.
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?

thanks, jo

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