Parameters | Copy Number | Sample Set(s) to Use for Subtraction

The One Set of Control Samples method calculates a summary statistic for the intensities (or counts) for a group of samples as defined by the parameter fields Variables Defining Analysis Groups and Control Levels, and subtract that value from each experimental sample measurement. 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 set in the Control Levels parameter field.The Multiple Sets of Control Samples option enables you to specify different sets of control samples to calculate the value for subtraction from different groups of experimental samples. You need to specify the variables that define the analysis groups, and then enter a subset of those variables as the 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 as the Control Levels. See the help for the Variables Defining Control Sets for more detail.The Control Samples Paired with Experimental Samples framework is 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: one column containing intensities (or counts) from normal tissue and one column containing measurements from a tumor tissue, and you want to subtract the normal tissue measurement from the tumor tissue measurement (for example. to interrogate loss of heterozygosity). In this case, the Sample ID variable and the Tumor (or Normal) variable in the Experimental Design SAS Data Set should be specified as Variables Defining Analysis Groups and the Tumor (or Normal) variable should be re-specified in the Variables Defining Control Sets field. The value indicating a tumor measurement should be specified in double quotation marks (“”) in the Control Levels field.