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 This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.

The most recent change is on probes with intensity at lower bounds. These use to go through the same adjustment for specific binding (GSB.adjust), but are no longer adjusted b/c they are believed to bear no signal. -- thanks to Wei Keat Lim and colleagues who brought it up in their paper "Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks" Lim et al, Bioinformatics 2007 Vol23(13):i282 Rullmann, J.A.C. (Ton) wrote: > 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 > > > > This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu