Control Set Design

Use this option to specify the experimental design framework of the control samples that will be used for subtraction from the experimental samples.

Available options are listed in the following table:

Select:	When you want to:
One Set of Control Samples	Calculate a summary statistic for the measurements for a group of samples and subtract that value from each sample measurement (control and experimental). You must specify the variables that define the analysis groups in the Variables Defining Analysis Groups field below and then enter the values of the analysis variables that define the group to be used as the control set in the Control Levels field.
Multiple Sets of Control Samples	Specify different sets of control samples to calculate values for normalization from different groups of experimental samples. You must specify the variables that define the analysis groups in the Variables Defining Analysis Groups field below and then enter a subset of those variables in the Variables Defining Control Sets field 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 the Control Levels field below.
Control Samples Paired With Experimental Samples	Include a specific case of multiple sets of control samples where each sample has multiple measurements (some of which are control, some of which are experimental). The basic case is where there are two columns per Sample ID and you want to subtract the measurement of one replicate from the other, In this case, the Sample ID variable and the Replicate variable in the experimental design data set should be specified in the Variables Defining Analysis Groups field and the Replicate variable should be re-specified in the Variables Defining Control Sets field. The value indicating a replicate measurement that you want to use as the control should be specified in double quotation marks in the Control Levels field.

To Select a Control Set Design:

Click the radio button corresponding to the design used in your experiment.