In certain chip images there are horizontal bands that are more prominant at the bottom of the chip.
I've written a program that extracts all probes with intensities over 10000
for a tiling chip hyb'ed with polyA mRNA and oligodT primed. I picked a cutoff
of 10000 because most of the intensities fell below 10000, except for the
bright bands seen on the DAT image. These data are attached. there are 6 columns
in these files. x, y, probe_seq, intensity,chromosome(or other id), chrPos
one is sorted by x coordinate.
the other file is sorted by y coordinate.
if you scroll through these files it is clear the common trait among the probes is the polyA run.
it is much easier to see the pattern in the file sorted by Y coordinate: