P-SCAN FAQ  

17 Nov 1999

1.  What are P and L in the output I get upon comparison of
multiple files?  Are they corrected intensities?  If so, how are they corrected?

P  refers to the average intensity of each spot where the average is taken over pixels within a circle of designated radius, centered at the lattice coordinates (P1) or at a nearby "optimal" location (P2) determined by a spot-finding algorithm.  L refers to the logarithms (base 10) of P.  A star in the variable name (P1*, L1*) indicates that the values have been normalized by (divided by) the median of all values for that particular image.

2.  In your experience, what fold over background constitutes a real signal?

For detecting spots (signal) on a background field, the determining factor is the noise level in the background.  This can be determined by evaluating several "spots" in regions of the image where signal is absent (e.g. the filter margins) and calculating the standard deviation, sigma.  Two- or three times sigma above background is a reasonable cutoff for determining real signal (spots).  Typically, if your eye can "see" a spot in an image, it is more than 2*sigma above background.

3.  What is used to calculate background?

Background can be determined by evaluating several "spots" in regions of the image where signal is absent (e.g. the filter margins) and calculating the standard deviation, sigma.  For practical purposes, background is often very close to the modal pixel value in an image. We often use the median pixel value instead of the mode, since it is much easier to calculate and gives a value slightly higer, but close to the background value.

4.  Is there any way to slope or bend the lines when snapping on the grids?

In PSCAN 1.0, there is no way to "bend" the lattice to fit curved lines within an array.  Nevertheless, it is usually possible to place a lattice on curved arrays and come sufficiently close to each point, so that the automatic spot location algorithm (P2) then finds the actual spot.  The spot-location algorithm is significantly improved in P-SCAN 1.2