Setting up a microarray experiment

To analyze differential expression, the Workbench must know which samples belong to which groups. This information is provided in an Experiment. Statistical analyses can then be carried out using the information in the Experiment to investigate differential expression. The Experiment element is also where things like t-test results and clustering information are stored.

The statistics created using this tool is for microarray data, RNA-Seq differential expression are better handled by the tools in the folder Toolbox | RNA-Seq and Small RNA Analysis (Image rna_seq_group_closed_16_n_p)

To set up an experiment:

        Toolbox | Microarray Analysis (Image expressionfolder)| Set Up Microarray 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 34.1).

Image setup_experiment_step1
Figure 34.1: Select the samples to use for setting up the experiment.

Clicking Next shows the dialog in figure 34.2.

Image setup_experiment_step2
Figure 34.2: 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 34.3.

Image setup_experiment_step3
Figure 34.3: Naming the groups.

Depending on the number of groups selected in figure 34.2, 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 34.4.

Image setup_experiment_step4
Figure 34.4: 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 34.2, 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 Finish to start the tool.