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.
