> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/setting-thresholds-and-background-sets.md).

# 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.


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