Low Hit Threshold

Categories in the output that have fewer than this number of hits are deleted.

Tip: Specify a 0 for this filter to have no effect.

Note the following process-specific information:

Process	Note
Gene Set Enrichment	Categories1 are deleted from the enrichment set for each of the tests specified2, according to whether each set fails to equal or exceed the cutoff specified here.3 Note: This filter is applied before the multiple testing adjustment. (See Multiple Testing Method for Adjusting p-Values and associated parameters.)
Gene Set Scoring	Categories4 having fewer than this number of hits are deleted from the output table. For example, setting this value to 10 computes gene set scores only for categories that contain at least ten genes.

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1

Specify categories using the Category Variables parameter.

2

Specify tests using the Enrichment Tests parameter.

3

Refer to Enrichment Tests for details about how these tests are performed. The deletion criterion is applied separately for each test, comparing the Low Hit Threshold to the following values: the sum of the Class 0 Count and Class 1 Count columns in the Output Data Set Containing Categories (if Fisher is chosen), the Frequency column in the Output Data Set Containing Categories (if Cochran-Armitage is chosen), and the _FREQ_ column in gsensum.sas7bdat (if PAGE is chosen). A deletion in one test might or might not correspond to a deletion in another test.

4

Categories are specified using the Category Variable parameter.

To Specify a Low Hit Threshold:

Type a threshold into the Low Hit Threshold text field.