Gene Set Scoring

Running this process for the AffymetrixLatinSquare sample setting generates the Results window shown below. Refer to the Gene Set Scoring process description for more information.

The Results window contains the following elements:

Output Data Set

One output data set (identified by the appended _gsc suffix) listing scores for each gene set is generated. The name and path to the data set are listed.

Click Open to open and view the data set.

The data set contains the following columns:

•	Category: This variable contains biological annotation generated from the input data set.

•	Frequency: This variable lists the number of probesets associated with each annotation category.

•	Multiple sample columns (shaded in yellow, above): Each column lists the category scores for a particular sample. A positive score indicates up-regulation of the genes in the specific category, as compared with baseline values. A negative score indicates down-regulation.

General

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.