Journal article

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

RA Irizarry, B Hobbs, F Collin, YD Beazer-Barclay, KJ Antonellis, U Scherf, TP Speed

BIOSTATISTICS | OXFORD UNIV PRESS | Published : 2003

Abstract

In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance-mean..

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University of Melbourne Researchers