Linear model for fast background subtraction in oligonucleotide microarrays.

Algorithms for Molecular Biology : AMB
K Myriam KrollE Carlon

Abstract

One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1) Correlated intensities between neighboring features in the chip and 2) sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.

References

Jun 10, 2003·Nature Biotechnology·Li ZhangKenneth D Aldape
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·G A HeldY Tu
Aug 26, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Felix Naef, Marcelo O Magnasco
Apr 19, 2005·Biophysical Journal·Hans Binder, Stephan Preibisch
Jan 18, 2006·Bioinformatics·Rafael A IrizarryHarris A Jaffee
Dec 16, 2006·Nucleic Acids Research·Li ZhangHaitao Zhao
Jul 23, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·K M KrollE Carlon
Jan 7, 2009·BMC Bioinformatics·Alessandro FerrantiniEnrico Carlon
Feb 24, 2009·BMC Bioinformatics·Geert C W M MuldersEnrico Carlon

❮ Previous
Next ❯

Citations

Dec 6, 2011·BMC Bioinformatics·Fabrice Berger, Enrico Carlon

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE4847
GSE8159
GSE7642
GSE9311
GSE3990

Methods Mentioned

BETA
chip
chips

Software Mentioned

GCRMA
R
MAS5
GC
Microarray Analysis Suite
Affymetrix
Bioconductor
Affymetrix MAS
RMA

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.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Zhijin Wu, Rafael A Irizarry
Proceedings of the National Academy of Sciences of the United States of America
G A HeldY Tu
© 2022 Meta ULC. All rights reserved