[BioC] justRMA() using different versions of affy

[Ben Bolstad]

I believe this issue has been touched on in the past:

https://stat.ethz.ch/pipermail/bioconductor/2008-December/025678.html

The only thing that should manifest in numerically different expression
values is that the quantile normalization code handles numerical ties
slightly differently than it did before. 

As for whether your XPS code, APT and anything else for that matter is
now getting it "wrong" . That is a decision I leave to independent
developers. I personally past the point of caring whether other
implementations of RMA have exact numerical agreement given the same
data input beyond those I wrote myself (eg the BioC/affy/preprocessCore
implementation and RMAExpress). The "RMA" brand name has been somewhat
diluted in its usage in the real world, being applied to all sorts of
things.

Best,
Ben


On Mon, 2009-06-29 at 23:17 +0200, cstrato wrote:
> 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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