Parameter estimation for the calibration and variance stabilization of microarray data

Statistical Applications in Genetics and Molecular Biology
Wolfgang HuberMartin Vingron

Abstract

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances of the transformed intensities become approximately independent of their expected values. The transformation is similar to the logarithm in the high intensity range, but has a smaller slope for intensities close to zero. Applications have shown better sensitivity and specificity for the detection of differentially expressed genes. In this paper, we describe the theoretical aspects of the method. We incorporate calibration and variance-mean dependence into a statistical model and use a robust variant of the maximum-likelihood method to estimate the transformation parameters. Using simulations, we investigate the size of the estimation error and its dependence on sample size and the presence of outliers. We find that the error decreases with the square root of the number of probes per array and that the estimation is robust against the presence of differentially expressed genes. Software is publicly available as an R package through the Bioconductor project (http://www.bioconductor.org).

Citations

Oct 20, 2005·Apoptosis : an International Journal on Programmed Cell Death·M SaundersB E Sawaya
Apr 23, 2004·Current Opinion in Biotechnology·Ted Holzman, Eugene Kolker
Nov 9, 2007·BMC Bioinformatics·Qi LiuYutaka Yasui
Nov 30, 2010·BMC Systems Biology·Gunnar SchrammRainer König
Sep 23, 2010·Genome Biology·Stefan ThomsenClaudio R Alonso
Sep 29, 2009·Mechanisms of Ageing and Development·Guorong LiPedro Gonzalez
Nov 30, 2006·Drug Discovery Today·Nicolas Fay
Apr 9, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Till SörensenThomas Häupl
May 20, 2006·The Plant Journal : for Cell and Molecular Biology·Cassandra S C CadmanWilliam E Finch-Savage
Jul 20, 2007·Biometrical Journal. Biometrische Zeitschrift·Mizanur R KhondokerBruce J Worton
Apr 13, 2013·Psychophysiology·Artur MatysiakReinhard König
Mar 3, 2015·The European Journal of Neuroscience·Reinhard KönigPeter Heil
Sep 22, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Erdem YörükLaurent Younes
Jan 3, 2006·International Journal of Developmental Neuroscience : the Official Journal of the International Society for Developmental Neuroscience·Uwe UeberhamThomas Arendt
Aug 17, 2005·Veterinary Immunology and Immunopathology·Dirk WerlingJoe Brownlie
Aug 12, 2008·The Journal of Thoracic and Cardiovascular Surgery·Volker RuppertUNKNOWN German Heart Failure Network
Dec 31, 2011·Acta Microbiologica Et Immunologica Hungarica·Dirk ProchnauJürgen Rödel
Sep 19, 2007·Arthritis Research & Therapy·Judith AuerHorst Ulrich Beuscher
Aug 31, 2007·FEMS Immunology and Medical Microbiology·Jürgen RödelEberhard Straube
Apr 9, 2005·IEEE Transactions on Nanobioscience·Rob D Coalson, Maria G Kurnikova
Dec 24, 2004·Journal of Bioinformatics and Computational Biology·Masato InoueShun-Ichi Amari
Dec 24, 2005·Journal of Bioinformatics and Computational Biology·Eugene Novikov, Emmanuel Barillot
Dec 10, 2016·Cytometry. Part B, Clinical Cytometry·Elena VendrameCatherine A Blish
Feb 18, 2017·Microarrays·Diana Mabel Kelmansky, Lila Ricci
Nov 17, 2011·Nucleic Acids Research·Javier Rodríguez-UbrevaEsteban Ballestar
Apr 13, 2010·Molecular & Cellular Proteomics : MCP·Natasha A KarpKathryn S Lilley
Jan 6, 2010·Statistical Methods in Medical Research·Zhijin Wu
Dec 5, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yunxia SuiZhijin Wu
Apr 26, 2005·Addiction Biology·Gordon Barr, Puhong Gao

❮ Previous
Next ❯

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.