[BioC] GCRMA Normalization Differences between Windows and MAC

Pierre Gestraud pierre.gestraud at curie.fr
Thu Jun 3 16:14:36 CEST 2010

I was wondering if there was an option to not use the adjustment
suggested by Lim in order to be consistent with some old analysis?

Zhijin Wu a écrit :
> We did make changes of the package over the years. One of the major
> changes is in the step of "gene specific binding (GSB) adjustment".
> This adjustment is done because probes have different efficiency in
> hybridization. At the background adjustment step, we do not really
> give probes 0 even if they appear to be mostly background, because of
> the trouble for log transformation. So those probes were shrunk to a
> lower bound parameter instead of 0. The original GSB adjustment was
> done on all probes. later we have decided to leave those probes at the
> lower bound un-adjusted because these were most likely background only
> (Thanks to  Lim et al, who discovered the problem and suggested the
> fix. see
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i282
> .)
> This change would mostly affect genes that are probably not expressed,
> but would also affect some genes that have a few very weak probes.
> best,
> Jean

Pierre Gestraud
Unité 900 Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer »
Institut Curie
26 rue d'Ulm - 75248 Paris Cedex 5
Tel: +33 (0) 1 56 24 69 25

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