In the final step, this integrated background value is subtracted from the raw integrated spot intensity to produce the background-subtracted integrated intensities we use for further analysis.

For all arrays, red and green channels were normalized by the medians of the distribution of spot intensities, and transformed to the zero time point of each individual time course.

When the spot intensity was close to the noisy background level, this model cannot be used to fit the data, due to near singularity of the matrix equations that had to be solved to perform the fitting.

Quantifying of the spot intensities was performed as indicated above.

The correlation between the values so obtained and the corresponding value of the integrated spot intensity from successful gaussian curve fitting was 0.99.

Most outliers in regular microarray were the results of spontaneous experimental error, with low spot intensities.

For instance, the maximum value of spot intensity is 65,000 in an Affymetrix scanner.

The reason that overall spot intensities in Fig.

Background-corrected intensity was computed by subtracting local background from spot intensity.

For each microarray, the background-corrected spot intensities were normalized by setting the 75th percentile equal to 1000.