[BioC] justRMA() using different versions of affy

[cstrato]

Dear all,

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?

Best regards
Christian
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