ABSTRACT
The basic requirement for a gene expression microarray experiment is that the measurement of intensities of each spot can in some way be interpreted to reflect the corresponding number of mRNA molecules in the sample under consideration. However, it is well known that raw intensity measurements are highly influenced by a number of different external factors, for example effects due to pins (1-3), PCR plates, sample preparation, array coating, spotting, labeling efficiencies, nonlinearity of dye-labeling, scanning, and so on (for an overview see 3, 4). Thus, it is obvious that raw intensity measurements of microarray spots typically do not reflect respective mRNA levels.
