[BioC] Different gcRMA results depending on platform and version

Zhijin Wu zwu at stat.brown.edu
Tue Feb 5 23:30:14 CET 2008

We did make differences on the gcRMA when we updated from 1.x.x to the 
2.x.x versions. Different results are expected because of the change in 
background estimation. However, assessment on the calibration data (two 
latin square datasets) showed that there is not much practical 
differences. For two samples, the differences in expression values from 
two different versions of gcrma should still be close to identical. (For 
example, you may see one gene used to be 6 and 6.1 across two samples 
and became 5 and 5.1 in another version, but the differences in 
expression are both .1).

> Hi, all,
> I just found gcRMA expression values for U133p2 arrays are different
> depending on platform and version.
> I compared two gcRMA expression values and they were quite different.
> The first one was by is R2.6.0, gcRMA 2.10.0, on Unix.
> The second one was obtained by R2.4.0, gcRMA 1.6.0, on WIndows XP.
> So, there was nothing in common between two, and I didn't try to figure out
> whether the difference came form platform difference or version difference
> (R or gcrma).
> Nonetheless, I was expecting consistent results regardless of platform of
> version.
> Has anyone noticed this?
> Thanks.
> JongMIn
> 	[[alternative HTML version deleted]]
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Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182

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