Equations 10 to 12 give Tmin, fmin, and K as functions of local background luminance L. For a background intensity value of 128, given a gamma-corrected display, the corresponding local background luminance is computed as follows: L = L min + 128 L max - L min M g (13).
The six intensities were averaged and a background intensity, taken from outside of the lens, was subtracted.
The immunoreactive signal intensity was analyzed with ImageJ software, with a grayscale background intensity of less than 20 (11.6 ± 0.55; mean ± s.e.m., max 19.9 gray).
To derive a p-value, some programs [ 7, 13] assume a globally uniform background intensity of tags, an assumption known to fail in ChIP experiments.
clusters) is studied via an auxiliary Poisson measure on the space of configurations in X="⊔nXn, with intensity measure defined as a convolution of the background intensity of cluster centres and the probability distribution of a generic cluster.
The centrosomal signal was defined by summing the intensity from an area representing the centrosome and subtracting the background intensity of an identical area.
Recruitment intensity was analyzed using a macro written for ImageJ that calculated the ratio of intensity of a circumscribed laser spot A to the adjacent area B such that an RFU for each data collection point was calculated by the equation RFU = (A − C /(B − C), where C is the background intensity of an unpopulated area of the image.
The local background intensities of all individual genes were subsequently averaged, resulting in the mean background intensity of a particular membrane.
URR coverage was defined as the percentage of spots called "present" when local background-subtracted intensity of a spot exceeded the average background intensity of all spots in that channel [ 31].
The Cy5 and Cy3 intensity channels were separately normalized using the mean difference between the median foreground intensity and the median background intensity of a set of representative probes.
