Setting up an experiment

To set up an experiment:

        Toolbox | Transcriptomics Analysis (Image expressionfolder)| Set Up Experiment (Image set_up_experiment)

Select the samples that you wish to use by double-clicking or selecting and pressing the Add (Image add) button (see figure 26.36).

Image setup_experiment_step1
Figure 26.36: Select the samples to use for setting up the experiment.

Note that we use "samples" as the general term for both microarray-based sets of expression values and sequencing-based sets of expression values (e.g. an expression track from RNA-Seq).

Clicking Next shows the dialog in figure 26.37.

Image setup_experiment_step2-biomedical
Figure 26.37: Defining the number of groups and expression value type.

Here you define the experiment type and the number of groups in the experiment.

The options are:

Clicking Next shows the dialog in figure 26.38.

Image setup_experiment_step3
Figure 26.38: Naming the groups.

Depending on the number of groups selected in figure 26.37, you will see a list of groups with text fields where you can enter an appropriate name for that group.

For multi-group experiments, if you find out that you have too many groups, click the Delete (Image close_x_red_16_n_p) button. If you need more groups, simply click Add New Group.

Click Next when you have named the groups, and you will see figure 26.39.

Image setup_experiment_step4
Figure 26.39: Putting the samples into groups.

This is where you define which group the individual sample belongs to. Simply select one or more samples (by clicking and dragging the mouse), right-click (Ctrl-click on Mac) and select the appropriate group.

Note that the samples are sorted alphabetically based on their names.

If you have chosen Paired in figure 26.37, there will be an extra column where you define which samples belong together. Just as when defining the group membership, you select one or more samples, right-click in the pairing column and select a pair.

Click Next if you wish to adjust how to handle the results. If not, click Finish.