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Table 4 Dye-swap reliability flag definition

From: The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

Dye-swap flag Conditions
Absent EST shows the p-call "A" in the Cy5 and Cy3 experiment
Non reliable The Cy5 and the Cy3 experiment show identical regulatory behavior (both UP, both DOWN)
Non regulated EST does not show any regulation in both experiments
TRUE EST shows "P" or "M" p-calls and is UP-regulated in the Cy5 and DOWN-regulated in the Cy3 experiment, or vice versa.
TRUE EST shows "P" p-call and is UP-regulated or DOWN-regulated in the, Cy5 while the Cy3 experiment shows a tendency towards the correct direction based on the ratio cut-off value, or vice versa
TRUE EST shows "P" or "M" p-call, but both experiments show NONE-regulated with one is UP-regulated or DOWN-regulated other is NONE-regulated, a tendency of regulation towards the correct direction based on a ratio cut-off
  1. ICEP determines a reliability flag by evaluating the P-call and regulation flags of ESTs. The reliability flag is used by ICEP to distinguish reliable from unreliable expression changes.