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

Biostatistics
Rafael A IrizarryTerence P Speed

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 relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure th...Continue Reading

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Oct 13, 2007·Nucleic Acids Research·Takeshi ObayashiKengo Kinoshita
Feb 27, 2008·Nucleic Acids Research·Hinanit Koltai, Carmiya Weingarten-Baror
Feb 4, 2009·Nucleic Acids Research·Javier CarreraAlfonso Jaramillo
Jan 9, 2010·Nucleic Acids Research·Wei ShiGordon K Smyth
Mar 20, 2009·Nucleic Acids Research·Yun-Shien LeeTzu-Hao Wang
Jun 17, 2009·Nucleic Acids Research·Dimos GaidatzisMichael B Stadler
Nov 13, 2009·Nucleic Acids Research·Ramil N NurtdinovAnna S Karyagina
Feb 13, 2010·Nucleic Acids Research·Hugues RichardMarie-Laure Yaspo
Feb 24, 2010·Nucleic Acids Research·María-José FerrándizAdela G de la Campa
Mar 24, 2010·Nucleic Acids Research·Joseph D DoughertyNathaniel Heintz
May 4, 2010·Nucleic Acids Research·Zhou DuZhen Su
Jun 24, 2010·Nucleic Acids Research·Lisa E M HopcroftAnna F Dominiczak
Jul 16, 2010·Nucleic Acids Research·Sarath Chandra Janga, Bruno Contreras-Moreira
Nov 17, 2011·Nucleic Acids Research·Javier Rodríguez-UbrevaEsteban Ballestar
Nov 30, 2011·Nucleic Acids Research·Pascal GellertShizuka Uchida
May 24, 2011·Nucleic Acids Research·Daniela NitschYves Moreau
Jul 7, 2011·Nucleic Acids Research·Debra L FultonAlan C Peterson
Jun 22, 2011·Nucleic Acids Research·Anna StinconeFrancesco Falciani
Jun 10, 2011·Nucleic Acids Research·Casey S Greene, Olga G Troyanskaya
Dec 4, 2012·Nucleic Acids Research·Takeshi ObayashiKengo Kinoshita
Nov 13, 2012·Nucleic Acids Research·Frederik Otzen BaggerBo T Porse
Dec 4, 2012·Nucleic Acids Research·Irina RusinovaPaul J Hertzog
Jan 12, 2013·Nucleic Acids Research·Andrew HarrisonAlexander E Pozhitkov
May 19, 2012·Nucleic Acids Research·Rosalind J CuttsClaude Chelala
Jun 7, 2012·Nucleic Acids Research·George C LindermanGurkan Bebek
Apr 6, 2013·Nucleic Acids Research·Yang LiaoWei Shi
Apr 20, 2013·Nucleic Acids Research·Charles D WardenYate-Ching Yuan
Apr 27, 2013·Nucleic Acids Research·Lars M T EijssenChris T Evelo
Apr 27, 2013·Nucleic Acids Research·Anna GoliszJoanna Kufel
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Apr 25, 2003·Nucleic Acids Research·Chen-An TsaiJames J Chen
May 26, 2005·Nucleic Acids Research·Chunlei WuLi Zhang
Dec 17, 2005·Nucleic Acids Research·Laura L EloTero Aittokallio
Jan 22, 2010·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Tali Zitman-Gal