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. Background Microarray technology is probably the most successful in the area of functional genomics. Biologists use it to analyze gene expression at the genome scale by comparing the levels of messenger RNAs present in matched biological sam...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes, Pierre Hilson
• Keywords: Background Microarray Technology, BMCBI 2004, Microarray Data, Spotting Effect