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Biology Direct

, 10:46



Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very complex, requiring sophisticated methods to control for various factors that are inherent to the procedures used. In this article we describe the individual steps of a microarray experiment, highlighting important elements and factors that may affect the processes involved and that influence the interpretation of the results. Additionally, we describe methods that can be used to estimate the influence of these factors, and to control the way in which they affect the expression estimates. A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results. By describing known factors which affect expression estimates this article provides guidelines for appropriate quality control and pre-processing of the data, additionally applicable to other transcriptome analysis methods that utilize similar sample handling protocols.

Reviewers: This article was reviewed by Dr. Janet Siefert, Dr. Leonid Hanin, and Dr. I King Jordan.

KeywordsMicroarrays Microarray pre-processing Quality control Transcriptome profiling Measurement bias Abbreviations3′IVT3′ in vitro transcription

3′-UTR3′ untranslated region

BGPBackground Intensity Probes

ChIPChromatin immunoprecipitation

cDNAComplementary DNA

ERCsExternal RNA controls


PCRPolymerase chain reaction

PMPerfect match

rRNARibosomal RNA

SNPSingle-nucleotide polymorphism

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Author: Roman Jaksik - Marta Iwanaszko - Joanna Rzeszowska-Wolny - Marek Kimmel

Source: https://link.springer.com/


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