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Alternatively, click on the Configure icon to access the advanced options (Figure 7). Number of data permutations (needed to calculate the normalised enrichment scores) can be controlled using the Permutations option. Permutation is to randomly permute the group assignment across a given gene. For each permutation, a random order is computed, that order is used to compute the score for each gene. Low value filter is turned on by default and will remove all the genes with the lowest average coverage of 1.0 or below; if a filter feature task was performed before this task, the default low-value filter is set to None (for details please see the GSA chapter) . Finally, if you start your project by importing a count matrix (i.e. as opposed to generating the count matrix using Partek Flow), you need to specify whether the expression values were log transformed before the import (use the Data has been log transformed with base drop down).

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