[BioC] Different gcRMA results depending on platform and version
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).
JONG-MIN LEE wrote:
> 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
> Has anyone noticed this?
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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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