Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited.
The expression level of each gene, relative to its median expression level across all conditions, was represented by a color, with red representing expression greater than the median, green representing expression less than the median, and color intensity representing the magnitude of the deviation from the median.
Note that this measures the deviation of the intensity of the SPD around the mean intensity, and not the deviation of the wavelength around its mean.
Applying variance stabilizing transforms may eliminate the intensity dependence of the standard deviation [ 38], but might also reduce statistical power or bias the test toward spots of certain intensities.
The new approach greatly simplifies the relationship between the intensity of the synchronous cross peak and the deviation terms caused by intermolecular interactions.
For the promoter arrays, we considered all the spots for which more than 70% of the pixels fluoresced with intensity above the median fluorescence intensity of the background plus two standard deviation and those showing enriched IP/control ratio >2 in all four slides were considered positive.
Threshold values were determined and applied by taking the mean pixel intensity of the profile plus one standard deviation, to remove spurious data points.
The intensity of the peak with the smallest deviation from the expected mass within a 10 ppm window was summed for each potential partner over the same MS range as the light species.
Low intensity signal spots (trimmed mean of raw intensity/trimmed mean of background < 1.5), uneven background (trimmed mean of raw intensity/standard deviation of background < 2.5), uneven spots (trimmed mean of raw intensity of background/standard deviation of raw intensity < 1) and spots that are not validated (flags) were removed from analysis before normalization.
(sigma_{0}) is the standard deviation (or intensity) of the noise, that for simplicity is supposed to be the same for all the neurons and constant in time.
