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Windowing/Thresholding
is used to detect clusters composed of enriched probes. The condition for
such a cluster is that it should contain at least a minimum number of
enriched probes (whose signal strength passes a threshold) and in the cluster
two consecutive probes should have a distance no more than a maximum gap. The
minimum number of probes, the maximum gap between two probes and the
threshold to judge enrichedness are all user-tuned parameters. The suggested
value for these parameters are 4 probes, 500 bps, and the mean plus 2.5 SD of
the raw log ratio data, respectively. |