The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

BMC Bioinformatics
Roel G W VerhaakDick de Ridder

Abstract

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. Using two publicly available datasets, i.e., gene-expression data of 285 patients with Acute Myeloid Leukemia (AML, Affymetrix HG-U133A GeneChip) and 42 samples of tumor tissue of the embryonal central nervous system (CNS, Affymetrix HuGeneFL GeneChip), we tested the effect of the four pre-processing strategies mentioned above, on (1) expression level measurements, (2) detection of differential expression, (3) cluster analysis and (4) classification of samples. In most cases, the effect of pre-processing is relatively small compared to other choices made in an analysis for the AML dataset, but h...Continue Reading

References

Jan 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·C Li, W H Wong
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Mar 29, 2002·The Hematology Journal : the Official Journal of the European Haematology Association·B A Van der ReijdenJ H Jansen
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Robert TibshiraniGilbert Chu
Oct 24, 2002·Blood·Sahar Barjesteh van Waalwijk van Doorn-KhosrovaniRuud Delwel
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Mar 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·John B WelshGarret M Hampton
Apr 15, 2003·The Hematology Journal : the Official Journal of the European Haematology Association·Sahar Barjesteh van Waalwijk van Doorn-KhosrovaniRuud Delwel
Aug 26, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Felix Naef, Marcelo O Magnasco
Feb 13, 2004·Bioinformatics·Leslie M CopeTerence P Speed
Apr 16, 2004·The New England Journal of Medicine·Lars BullingerJonathan R Pollack
Apr 16, 2004·The New England Journal of Medicine·Peter J M ValkRuud Delwel
May 8, 2004·Neural Computation·Tilman LangeJoachim M Buhmann
Feb 26, 2005·Proceedings of the National Academy of Sciences of the United States of America·James C MulloyStephen D Nimer
Apr 20, 2010·Bioinformatics·Ashok SharmaRichard A McIndoe

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Citations

Oct 31, 2006·Omics : a Journal of Integrative Biology·Steffen Heber, Beate Sick
Mar 26, 2011·PloS One·Xin Victoria WangTerence P Speed
Dec 11, 2007·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Suzanne K LauMing-Sound Tsao
Feb 19, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Zhifu SunPing Yang
Jan 18, 2007·The Plant Journal : for Cell and Molecular Biology·Kevin M CulliganAnne B Britt
May 28, 2010·Journal of Cellular Physiology·Jose Diaz-RomeroPierre Mainil-Varlet
Jul 16, 2010·Angewandte Chemie·William J GriffithsHans-Peter Deigner

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Datasets Mentioned

BETA
GSE1159

Methods Mentioned

BETA
chip
PCR

Software Mentioned

PLIER
MicroArray Suite ( MAS
GeneLogic
Bioconductor
GCOS
PAM
MAS
Significance Analysis of Microarrays ( SAM )
LIKNON
R

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