title: Comments on selected fundamental aspects of microarray analysis.
abstract: Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone.
authors.affiliation: Laboratoire Génome et Informatique UMR 8116 Tour Evry2, 523 Place des Terrasses, 91034 Evry Cedex, France. gucki@genopole.cnrs.fr
authors.forename: Alessandra
authors.initials: A
authors.lastname: Riva
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Carpentier
authors.forename: Bruno
authors.initials: B
authors.lastname: Torrésani
authors.forename: Alain
authors.initials: A
authors.lastname: Hénaut
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D046228:Microarray Analysis / Q000379:methods / Q000706:statistics & numerical data; D015999:Multivariate Analysis; D025341:Principal Component Analysis / Q000379:methods; D012107:Research Design; D012984:Software