title: Spotting effect in microarray experiments.
abstract: BACKGROUND
  Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array.
  
  
  RESULTS
  Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure.
  
  
  CONCLUSIONS
  The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.
authors.affiliation: Institut National Agronomique Paris-Grignon, 75231 Paris, France. maryhuar@inapg.fr
authors.forename: Tristan
authors.initials: T
authors.lastname: Mary-Huard
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Daudin
authors.forename: Stéphane
authors.initials: S
authors.lastname: Robin
authors.forename: Frédérique
authors.initials: F
authors.lastname: Bitton
authors.forename: Eric
authors.initials: E
authors.lastname: Cabannes
authors.forename: Pierre
authors.initials: P
authors.lastname: Hilson
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics; D030541:Databases, Genetic / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards* / Q000706:statistics & numerical data; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D016011:Normal Distribution; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards* / Q000706:statistics & numerical data; D010963:Plasmodium falciparum / Q000235:genetics; D012107:Research Design / Q000592:standards / Q000706:statistics & numerical data
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D016054:DNA, Protozoan