Quantification of expression: cDNA arrays
For each spot on the slide we use image analysis to calculate
Red intensity = Rfg - Rbg, Green intensity = Gfg - Gbg
fg = foreground, bg = background, and and combine them in
the log (base 2) expressions:
M = log2( Red intensity / Green intensity) [log fold change]
A = log2 v (Red intensity ? Green intensity) [abundance]
Issues: image analysis, esp. bg determination; to subtract bg or not?; to log or not?; filtering/quality?