title: Sources of variation in Affymetrix microarray experiments.
abstract: BACKGROUND
  A typical microarray experiment has many sources of variation which can be attributed to biological and technical causes. Identifying sources of variation and assessing their magnitude, among other factors, are important for optimal experimental design. The objectives of this study were: (1) to estimate relative magnitudes of different sources of variation and (2) to evaluate agreement between biological and technical replicates.
  
  
  RESULTS
  We performed a microarray experiment using a total of 24 Affymetrix GeneChip arrays. The study included 4th mammary gland samples from eight 21-day-old Sprague Dawley CD female rats exposed to genistein (soy isoflavone). RNA samples from each rat were split to assess variation arising at labeling and hybridization steps. A general linear model was used to estimate variance components. Pearson correlations were computed to evaluate agreement between technical and biological replicates.
  
  
  CONCLUSIONS
  The greatest source of variation was biological variation, followed by residual error, and finally variation due to labeling when *.cel files were processed with dChip and RMA image processing algorithms. When MAS 5.0 or GCRMA-EB were used, the greatest source of variation was residual error, followed by biology and labeling. Correlations between technical replicates were consistently higher than between biological replicates.
authors.affiliation: University of Alabama, Birmingham, Alabama, USA. szakharkin@ms.soph.uab.edu
authors.forename: Stanislav O
authors.initials: SO
authors.lastname: Zakharkin
authors.forename: Kyoungmi
authors.initials: K
authors.lastname: Kim
authors.forename: Tapan
authors.initials: T
authors.lastname: Mehta
authors.forename: Lang
authors.initials: L
authors.lastname: Chen
authors.forename: Stephen
authors.initials: S
authors.lastname: Barnes
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Scheirer
authors.forename: Rudolph S
authors.initials: RS
authors.lastname: Parrish
authors.forename: David B
authors.initials: DB
authors.lastname: Allison
authors.forename: Grier P
authors.initials: GP
authors.lastname: Page
mesh_terms: D000818:Animals; D039301:Computers, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results