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For One Set of Control Samples, you need to specify the variables that define the analysis groups and then enter the values of the analysis variables that define the group to be used as the control in the Control Levels parameter field. Samples belonging to the control group are used to compute the reference level for each gene.
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The Multiple Sets of Control Samples option enables you to calculate different reference levels for different groups of samples. You need to specify the variables that define the analysis groups, and then enter a subset of those variables as Variables Defining Control Sets to specify which groups of samples within the analysis groups should be used for computing the reference levels. The values that indicate the controls of the variables that define the control sets should be entered in as Control Levels. See the Help for the Variables Defining Control Sets for more detail.
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Specifying Summary Statistic Over All Samples uses all samples to compute the reference level for each gene or row.
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