[BioC] justRMA() using different versions of affy
cstrato at aon.at
Mon Jun 29 23:17:37 CEST 2009
Maybe this question has been answered long time ago, but I have just
tested function justRMA() with different versions of package affy and
found the following behavior:
The results obtained with version affy_1.14.2 for BioC 2.0 and earlier
versions are different from the results obtained with version
affy_1.16.0 for BioC 2.1 and later versions. Interestingly, affy_1.16.0
is the first version to use the new package preprocessCore.
When comparing these versions of affy to the newest version of the
Affymetrix Power Tools (apt-1.10.2) or to xps it turns out that the
results are identical to the old implementation affy_1.14.2, but differ
from newer implementations of package affy.
Although the difference is less than 0.5% I would nevertheless like to
know what causes this difference. I have always assumed that only
certain source code has been moved from affy to preprocessCore but did
not expect to see a difference in the results obtained.
Do you know what causes this difference and why?
Is there a difference in the background calculation, quantile
normalization or median-polish summarization?
Or is there a difference in the usage of probes for background
calculation and/or quantile normalization?
e.m.a.i.l: cstrato at aon.at
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