The Effect of Probe Length and GC% on Microarray Signal Intensity: Characterizing the Functional Relationship

摘要: The quality of a microarray experiment is measured by sensitivity and specificity which depend on hybridization efficiency non-specific cross-hybridization. length GC% probe sequences are known to strongly affect However, the joint effect both signal intensity has not been systematically assessed. Here I use set yeast data with varying from 12.5% 68.75% 27 40nt simultaneously assess DNA hybridization. Both have significant impact (SI) model derived shows how changes in can be compensated why such compensation did work some previous studies. SI increases sigmoidally based where constant. Our characterization suggests new ways design microarrays normalize reduce error variation.