[BioC] Two rma questions
jmacdon at med.umich.edu
Thu Apr 15 14:50:28 CEST 2004
For your first question, it is almost always preferable to run rma on
all samples in a set together rather than in two batches. For the second
question, the bug only concerns justRMA and justGCRMA, so rma and gcrma
are not affected.
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
>>> Simon Kidd <kidd at mail.rockefeller.edu> 04/14/04 11:35AM >>>
We have been comparing the effects of a mutation to two different
duplications of the wild type gene (ie g- v g-/dp1(g+) and g- v
g-/dp2(g+)) and then doing rma on either the pooled affy chips or the
two genotypes separately and then pooling them for analysis in dChip.
But which of the methods, separate or together is the statistically
the correct way of doing the rma analysis? The two give different
numbers of differentially expressed genes.
The second question, does rma in affy v1.4.21 have the same bug as
justRMA and gcRMA in affy v1.4.22?
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