Setting Thresholds and Background Sets

• Select an experiment, right click and activate Properties...

  • The page displayed indicates information about that experiment. There is a place to enter notes or descriptions, the number of IDs in play are also listed as is the Threshold and P-Threshold.

• Threshold refers to the fold-change or log ration cutoff that is in play.

• Select all three experiments in the ColonMet_Faked folder and activate Tools-->Set Threshold and Background List. Next to General, Enter 1 in the Threshold and 0.1 in the P Threshold. Leave background option at default and click OK.

  • If an array is the source of the data, the background list can be set to the gene content of the array, otherwise the default behavior is to use everything.

• Use the right-click, properties function to confirm that threshold settings have been set for each experiment.

• Activate the ColonMet_Faked_FC experiment and refresh the page so that it is visible in the Active Data panel.

• Select the experiment in the active data panel and click Tools-->Set Threshold and Background List. Click the statistics button. Counts of pass-threshold items in various categories are displayed. The signal distribution button will show the data for these faked values.