Hi, 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? best, Pierre Zhijin Wu a ?crit : > 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 Unit? 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