Microarray experiments and factors which affect their reliability.
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.
Systems Biology Group, Faculty of Automatic Control, Electronics and Informatics, Silesian University of Technology, Gliwice, Poland. roman.jaksik@polsl.pl.
Roman
R
Jaksik
Systems Biology Group, Faculty of Automatic Control, Electronics and Informatics, Silesian University of Technology, Gliwice, Poland. marta.iwanaszko@polsl.pl.|Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. marta.iwanaszko@polsl.pl.|Department of Statistics, Rice University, Houston, TX, USA. marta.iwanaszko@polsl.pl.
Marta
M
Iwanaszko
Systems Biology Group, Faculty of Automatic Control, Electronics and Informatics, Silesian University of Technology, Gliwice, Poland. joanna.rzeszowska-wolny@polsl.pl.
Joanna
J
Rzeszowska-Wolny
Systems Biology Group, Faculty of Automatic Control, Electronics and Informatics, Silesian University of Technology, Gliwice, Poland. kimmel@rice.edu.|Department of Statistics, Rice University, Houston, TX, USA. kimmel@rice.edu.
Marek
M
Kimmel
D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards; D015203:Reproducibility of Results