Calibration of microarray gene-expression data

Item Type:	Article
Title:	Calibration of microarray gene-expression data
Creators Name:	Binder, H. and Preibisch, S. and Berger, H.
Abstract:	Calibration of microarray measurements aims at removing systematic biases from the probe-level data to get expression estimates that linearly correlate with the transcript abundance in the studied samples. The improvement of calibration methods is an essential prerequisite for estimating absolute expression levels, which, in turn, are required for quantitative analyses of transcriptional regulation, for example, in the context of gene profiling of diseases. We address hybridization on microarrays as a reaction process in a complex environment and express the measured intensities as a function of the input quantities of the experiment. Popular calibration methods such as MAS5, dChip, RMA, gcRMA, vsn, and PLIER are briefly reviewed and assessed in light of the hybridization model and of previous benchmark studies. We present our hook method, a new calibration approach that is based on a graphical summary of the actual hybridization characteristics of a particular microarray. Although single-chip related, hook performs as well as the multi-chip-related gcRMA, presently one of the best state-of-the-art methods for estimating expression values. The hook method, in addition, provides a set of chip summary characteristics that evaluate the performance of a given hybridization. The algorithm of the method is briefly described and its performance is exemplified.
Keywords:	Gene Expression, Microarray Calibration, Preprocessing Methods, Transcript Concentration, Hook Curve, Hybridization, Langmuir Isotherm
Source:	Methods in Molecular Biology
Series Name:	Methods in Molecular Biology
Title of Book:	Cancer Gene Profiling
ISSN:	1064-3745
ISBN:	978-1-934115-76-3
Publisher:	Springer / Humana Press
Volume:	576
Page Range:	375-407
Date:	2010
Official Publication:	https://doi.org/10.1007/978-1-59745-545-9_20
PubMed:	View item in PubMed

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