Hi, In re-running gcrma (using defaults) on some mgu74av2 cel files, I'm getting different results using version 1.1.3, than were gotten earlier with 1.1.0. The versions of the cdf and probe packages are the same, so I'm wondering what has changed in the gcrma package. I don't mind looking through the code for changes, but was hoping someone could enlighten me as to the specific changes. Thanks, Peter Peter Lambert Statistician Agilent Technologies http://www.silicongenetics.com

The change is made in the way background parameters were estimated. The idea is the same except we used to take local quantiles for bins of probe affinity levels, and in 1.1.3 we used loess curve. I should make available a vignette explaining that, hopefully in March. Best, Jean On Fri, 28 Jan 2005 peter_lambert@agilent.com wrote: > Hi, > > In re-running gcrma (using defaults) on some mgu74av2 cel files, I'm > getting different results using version 1.1.3, than were gotten earlier > with 1.1.0. The versions of the cdf and probe packages are the same, so > I'm wondering what has changed in the gcrma package. I don't mind > looking through the code for changes, but was hoping someone could > enlighten me as to the specific changes. > > Thanks, > Peter > > > Peter Lambert > Statistician > Agilent Technologies > http://www.silicongenetics.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >