Hi, Has anybody used the single-array error model described in the supplemental material of Hughes et al., Cell, 102, 109 (2000)? It models uncertainties in individual arrays, and is widely used in ChIP- chip analysis. I would like to know if anybody has used it and liked it and if it is implemented in R. This method was also used in Ren et al., Science (2000), 290, 2306 Lee et al. Science (2002), 298, 799 Li et al., PNAS (2003), 100, 8164 ... Thanks, Françoise Thibaud-Nissen [[alternative HTML version deleted]]

Hi Francoise, are you aware of a sufficiently detailed description of that error model, which would allow to estimate its parameters from data? I think that the additive-multiplikative error model by Blythe Durbin and David Rocke is related to that of Hughes et al.: Rocke DM, Durbin B. A model for measurement error for gene expression arrays. J Comput Biol. 2001;8(6):557-69. PMID: 11747612 But I would be happy to be corrected if I am wrong. The Rocke-Durbin model is used in the package "vsn" for the estimation of background correction and normalization parameters, and can be used to derive attenuated log-ratios that have intensity-independent variance. See also: http://www.bepress.com/bioconductor/paper6 Best regards Wolfgang <quote who="Thibaud-Nissen, Francoise"> > Hi, > > > > Has anybody used the single-array error model described in the > supplemental material of Hughes et al., Cell, 102, 109 (2000)? It models > uncertainties in individual arrays, and is widely used in ChIP-chip > analysis. > > > > I would like to know if anybody has used it and liked it and if it is > implemented in R. > > > > This method was also used in > > Ren et al., Science (2000), 290, 2306 > > Lee et al. Science (2002), 298, 799 > > Li et al., PNAS (2003), 100, 8164 > > ... > > > > Thanks, > > > > Fran?oise Thibaud-Nissen > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.ebi.ac.uk/huber