Spotting effect in microarray experiments.
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.
Mary-Huard
Tristan
T
Institut National Agronomique Paris-Grignon, 75231 Paris, France. maryhuar@inapg.fr
Daudin
Jean-Jacques
JJ
Robin
Stéphane
S
Bitton
Frédérique
F
Cabannes
Eric
E
Hilson
Pierre
P
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
D018076:DNA, Complementary; D018744:DNA, Plant; D016054:DNA, Protozoan