[BioC] rma on affy experiment with different cell lines

James MacDonald jmacdon at med.umich.edu
Fri Jul 16 16:15:55 CEST 2004

We commonly compare multiple cell lines in a single experiment using
rma. The goal is different (which genes are differentially expressed in
the different cell lines). However, I have never seen anything that
indicated that normalizing different cell lines together was a bad



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

>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 07/16/04
05:01AM >>>

has anyone experience how good rma performs on affymetrix experiments
where the
data from different cell lines are compared against each other?
i have 4 chips, one with cell line 1 with treatment, one with cell line
without treatment, one with cell line 2 with treatment and one with
cell line 2
without treatment. the question is, should i normalize all them
together using
rma, or should i normalize cell line 1 (+/- treatment) and cell line 2
treatment) separatly.
As i have no replicates, i am hoping, as the cell lines are not that
that the model parameters are better fitted into the data.

thanks, jo

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