title: Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis.
abstract: BACKGROUND
  Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analyses. However, the amount of work done to integrate and evaluate these tools and the corresponding experimental procedures is not high. Although complex hybridization experiments are based on a data production pipeline that incorporates a significant amount of error parameters, the evaluation of these parameters has not been studied yet in sufficient detail.
  
  
  RESULTS
  In this paper we present simulation studies on several error parameters arising in complex hybridization experiments. A general tool was developed that allows the design of exactly defined hybridization data incorporating, for example, variations of spot shapes, spot positions and local and global background noise. The simulation environment was used to judge the influence of these parameters on subsequent data analysis, for example image analysis and the detection of differentially expressed genes. As a guide for simulating expression data real experimental data were used and model parameters were adapted to these data. Our results show how measurement error can be balanced by the analysis tools.
  
  
  CONCLUSIONS
  We describe an implemented model for the simulation of DNA-array experiments. This tool was used to judge the influence of critical parameters on the subsequent image analysis and differential expression analysis. Furthermore the tool can be used to guide future experiments and to improve performance by better experimental design. Series of simulated images varying specific parameters can be downloaded from our web-site: http://www.molgen.mpg.de/~lh_bioinf/projects/simulation/biotech/
authors.affiliation: Department of Vertebrate Genomics, Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin-Dahlem, Germany. wierling@molgen.mpg.de
authors.forename: Christoph K
authors.initials: CK
authors.lastname: Wierling
authors.forename: Matthias
authors.initials: M
authors.lastname: Steinfath
authors.forename: Thorsten
authors.initials: T
authors.lastname: Elge
authors.forename: Steffen
authors.initials: S
authors.lastname: Schulze-Kremer
authors.forename: Pia
authors.initials: P
authors.lastname: Aanstad
authors.forename: Matthew
authors.initials: M
authors.lastname: Clark
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Ralf
authors.initials: R
authors.lastname: Herwig
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000196:embryology / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D003198:Computer Simulation; D018076:DNA, Complementary / Q000032:analysis; D018744:DNA, Plant / Q000032:analysis; D020869:Gene Expression Profiling / Q000592:standards / Q000706:statistics & numerical data; D018745:Genome, Plant; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards / Q000706:statistics & numerical data; D012107:Research Design / Q000592:standards / Q000706:statistics & numerical data
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant