[BioC] Different gcrma output values after upgrade BioC 2.0 -> 2.4

[Rullmann, J.A.C. (Ton)]

Hi,
We upgraded from BioC 2.0 to BioC 2.4. Now I note that log-intensities
computed by gcrma differ from the values I got previously, for the same
input.
For example, for one array the mean ratio of old vs new log-intensities
is 0.9996 with an sd of 0.0187.
For a second array, analyzed in the same set, the mean and sd values are
0.9991 and 0.0197.
This implies there are dozens of probe sets for which the computed
log-intensity changes by ~ 10%.

Is this "expected behaviour", that is: has the gcrma algorithm changed?

Thanks,

Ton Rullmann
Senior Research Scientist
Project Leader Systems Biology
Dept. Molecular Design and Informatics
Schering-Plough
RK 2309
PO Box 20
5340 BH Oss, The Netherlands
www.schering-plough.com



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