I'm not sure if there is such a thing as a "correct" definition. A formal definition -by definition- cannot be correct or incorrect. Anyways, the purposes of Background Correction and PM Correction, respectively, are indeed very similar. They are designed to estimate non-specific signal contributions such as unspecific binding, cross- hybridization and auto-fluorescence of the surface. The difference is that PM correction is specific to the Affymetrix microarray design where each PM probe is (or used to be) complimented by a mismatch probe. If and how you incorporate this sequence-specific information into your model determines how much you separate the two preprocessing steps. HTH, --Johannes Johannes Freudenberg Graduate Student Division of Biomedical Informatics TCHRF 8526 Cincinnati Children's Hospital Medical Center 3333 Burnet Avenue Cincinnati, OH 45229 phone: (513) 636-1424 fax: (513) 636-2056 e-mail: johannes.freudenberg at cchmc.org >>> Mohammad Esad-Djou <shahrgol at="" web.de=""> 11/21/06 9:54 AM >>> Hello All, I would like to separate tasks of Background Correction and PM Correction in Preprocessing methods. Unfortunately I do not find a uniform definition in literature. Sometimes are tasks of PM Correction and Background Correction similarly, e.g. Correction of Cross hybridisation. Where and how can I clear (and correct!) Definition about it find? Thanks, Mohammad Interdisciplinary Centre for Bioinformatics University of Leipzig H?rtelstr. 16 - 18 D-04107 Leipzig _______________________________________________ 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