Adjusting batch effects in microarray expression data using empirical Bayes methods

Biostatistics
W Evan JohnsonAriel Rabinovic

Abstract

Non-biological experimental variation or "batch effects" are commonly observed across multiple batches of microarray experiments, often rendering the task of combining data from these batches difficult. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict sample size or in studies that require the sequential hybridization of arrays. In general, it is inappropriate to combine data sets without adjusting for batch effects. Methods have been proposed to filter batch effects from data, but these are often complicated and require large batch sizes ( > 25) to implement. Because the majority of microarray studies are conducted using much smaller sample sizes, existing methods are not sufficient. We propose parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples. We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://bios...Continue Reading

References

Jan 23, 1999·Nature Genetics·E S Lander
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
May 8, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A NewtonK W Tsui
Apr 20, 2002·Lancet·Torsten O NielsenMatt van de Rijn
Nov 25, 2003·Analytical Chemistry·Thomas L FareYanqun Wang
Dec 25, 2003·Bioinformatics·Monica BenitoJ S Marron
Jun 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daniel R RhodesArul M Chinnaiyan
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

❮ Previous
Next ❯

Citations

Sep 29, 2011·Theory in Biosciences = Theorie in Den Biowissenschaften·Alina SîrbuMartin Crane
Jun 23, 2012·Leukemia·R KuiperP Sonneveld
Nov 14, 2012·Molecular Psychiatry·C ChenC Liu
May 24, 2013·Nature·Matthew R HepworthGregory F Sonnenberg
Jan 17, 2012·Nature Cell Biology·Tim AhfeldtChad A Cowan
Nov 21, 2013·Nature Communications·Todd LenczAriel Darvasi
Sep 11, 2012·Nature Immunology·Youjin LeeVijay K Kuchroo
Oct 14, 2008·Nature Neuroscience·Michael C OldhamDaniel H Geschwind
May 28, 2013·Nature Neuroscience·Elizabeth M BradshawPhilip L De Jager
Sep 15, 2010·Nature Reviews. Genetics·Jeffrey T LeekRafael A Irizarry
Sep 19, 2012·Nature Reviews. Genetics·Christoph Bock
Feb 19, 2013·Nature Structural & Molecular Biology·Harry G LeitchPetra Hajkova
Jun 4, 2013·Nature Structural & Molecular Biology·Zhou DuX Shirley Liu
Dec 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Katherine S GarmanAnil Potti
May 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Divya MehtaElisabeth B Binder
May 30, 2009·The Journal of Biological Chemistry·Tong ZhangW Lee Kraus
Dec 5, 2012·The Journal of Biological Chemistry·Johanna TahvanainenRiitta Lahesmaa
Nov 9, 2011·The Journal of Experimental Medicine·Marina CaskeyRafick P Sékaly
Oct 24, 2012·The Journal of Experimental Medicine·Marc SeifertRalf Küppers
Jul 3, 2013·Omics : a Journal of Integrative Biology·Bedilu Alamirie EjiguMaya Berg
Jan 6, 2012·Annals of Oncology : Official Journal of the European Society for Medical Oncology·E FountzilasD Spentzos
Sep 13, 2012·Annals of Oncology : Official Journal of the European Society for Medical Oncology·P M McGowanM J Duffy
Aug 2, 2012·Briefings in Bioinformatics·Cosmin LazarAnn Nowé
Nov 30, 2012·Briefings in Bioinformatics·Yunda Huang, Raphael Gottardo
Mar 8, 2008·Bioinformatics·Andrey A ShabalinAndrew B Nobel
Apr 8, 2010·Bioinformatics·Gábor CsárdiSven Bergmann
Jun 21, 2011·Bioinformatics·Phuong DaoS Cenk Sahinalp

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.