[BioC] tasks of Background Correction and PM Corr =?iso-8859-15?q?ection_in_Prepro

[Johannes Freudenberg]

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 
Härtelstr. 16 - 18
D-04107 Leipzig

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