title: Microarrays: how many do you need?
abstract: We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current knowledge allows for the construction of models that look realistic with respect to searches for individual differentially expressed genes and derive prototypical parameters from real data sets. Such models allow investigation of the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class, the fold changes in expression that are desired to be detected, the detection sensitivity of the microarrays, and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at www.scai.fhg.de/special/bio/howmanyarrays/ for fine tuning simulations to their particular settings.
authors.affiliation: Max-Planck-Institut für biologische Kybernetik, Spemannstrasse 38, 72076 Tübingen, Germany. Alexander.Zien@tuebingen.mpg.de
authors.forename: Alexander
authors.initials: A
authors.lastname: Zien
authors.forename: Juliane
authors.initials: J
authors.lastname: Fluck
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012107:Research Design; D015983:Selection Bias; D018709:Statistics, Nonparametric