Model-based variance-stabilizing transformation for Illumina microarray data

Nucleic Acids Research
Simon M LinWarren A Kibbe

Abstract

Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achieving variance stabilization can be difficult. Although the Illumina microarray platform provides a larger number of technical replicates on each array (usually over 30 randomly distributed beads per probe), these replicates have not been leveraged in the current log2 data transformation process. We devised a variance-stabilizing transformation (VST) method that takes advantage of the technical replicates available on an Illumina microarray. We have compared VST with log2 and Variance-stabilizing normalization (VSN) by using the Kruglyak bead-level data (2006) and Barnes titration data (2005). The results of the Kruglyak data suggest that VST stabilizes variances of bead-replicates within an array. The results of the Barnes data show that VST can improve the detection of differentially expressed genes and reduce false-positive identifications. We conclude that although both VST and VSN are built upon the same model of measurement noise, VST stabilizes the variance better and m...Continue Reading

References

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Citations

May 11, 2010·Journal of Cancer Research and Clinical Oncology·Maximo A BenavidesMaarten C Bosland
Sep 24, 2010·ACS Nano·Matthew D MassichChad A Mirkin
Dec 10, 2013·Nature Genetics·Chi C WongDavid J Adams
Jun 24, 2009·The Pharmacogenomics Journal·H Landmark-HøyvikV Dumeaux
Dec 1, 2010·Proceedings of the National Academy of Sciences of the United States of America·Carolyn A de GraafDouglas J Hilton
Jun 7, 2013·Tissue Engineering. Part a·Sarah SundelacruzDavid L Kaplan
May 10, 2008·Bioinformatics·Pan DuSimon M Lin
Feb 6, 2009·Bioinformatics·Yang XieMichael Story
Dec 21, 2010·Bioinformatics·Ryung S Kim, Juan Lin
Mar 10, 2012·Human Molecular Genetics·Chris WallaceStefan Blankenberg
Mar 2, 2011·The Journal of Infectious Diseases·Kristine L BucasasJohn W Belmont
Nov 20, 2009·Nucleic Acids Research·Nuno L Barbosa-MoraisSimon Tavaré
Oct 13, 2010·Infection and Immunity·Matthew J BurtonRobin L Bailey
Jun 1, 2012·Journal of Virology·Brian P DoehleMichael Gale
Jul 22, 2009·Molecular and Cellular Biology·Zan HuangJohn D Crispino
Dec 7, 2011·Molecular and Cellular Biology·Nikita AvvakumovJacques Côté
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Dec 2, 2010·BMC Bioinformatics·Matthias Kohl, Hans-Peter Deigner
Feb 26, 2013·BMC Bioinformatics·Jan P Meier-KolthoffMarkus Göker

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Methods Mentioned

BETA
chip
chips

Software Mentioned

Illumina BeadStudio
VST
VSN
limma
BeadStudio
MIAME
Bioconductor ‘ limma
Bioconductor

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