Local background

Local backgrou...

Array level quality control

•Problems: –array fabrication defect –problem with RNA extraction –failed labeling reaction –poor hybridization conditions –faulty scanner – •Quality measures: –Percentage of spots with no signal (~30% excluded spots) –Range of intensities –(Av. Foreground)/(Av. Background) > 3 in both channels –Distribution of spot signal area –Amount of adjustment needed: signals have to substantially changed to make slides comparabl...

Introduction Microarray Analysis

Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish. The benefits of using this plant in biology are the small genome size (125 Mb), the extensive chromosome maps, short life cycle, and the large number of mutant line resources available (NIH 2012). All of these properties...