Toolbox | Tools | Transcriptomics Analysis ()| Set Up Experiment ()
The output from the tool is an experiment, which essentially is a set of samples that are grouped. When setting up the experiment, you define the relationship between the samples. This makes it possible to do statistical analysis to investigate the differential expression between the groups. The experiment is also used to accumulate calculations like t-tests and clustering because this information is closely related to the grouping of the samples.
How to set up an experiment is described in detail in the Biomedical Genomics Workbench reference manual under "Setting up an experiment" in Chapter "Transcriptomics Analysis".