What do the expression levels mean?
Different oligonucleotide probes have different hybridization properties. This means that one oligonucleotide complementary to one part of a transcript may give a strong signal while another oligonucleotide complementary to a different part of the same transcript may give a weak signal, even if the oligonucleotides were designed to have similar GC-content and thermostabilities. These differences may be the result of secondary structure in the target. Thus most people generally believe that one cannot estimate a gene’s expression level by measuring the signal intensity from a single probe. However, by examining the distribution of a probeset’s signal intensities we can make an educated guess about transcript levels. For our array, low levels are below 100, moderate 100 to 1000 and above 1000, very high. These are estimates obtained by integrating all of the information from a set of probes. The quality of these predictions decreases for genes with only one or two probes.
