Running the Analyze Expression Data and Upload Comparisons to IPA Workflow

The workflow can be started from the toolbox, or by using the Launch button (Image launch_16_n_p).

Choose the expression data to be analyzed and uploaded (see figure 4.7).

Image ipawf_step1
Figure 4.7: Selecting input parameters in the IPA plugin workflow.

Following this, the parameters for the Differential Expression for RNA-Seq need to be specified (see figure 4.8):

Image ipawf_step2
Figure 4.8: Selecting parameters for Differential Expression for RNA-Seq.

Metadata table
Select a metadata object that associates the selected input objects to metadata used by the RNA-Seq analysis.
Test differential expression due to
Select the factor to be tested for differential expression.
Select groups to be compared. It is possible to choose between "Across groups", "All group pairs", and "Against control group".
Control group
If "Against control group" was selected in "Comparisons", a control group must be selected.

An example of a metadata table is shown in figure 4.9.

Image IPA-WF-metadata_table
Figure 4.9: An example of a metadata table.

Metadata is required when defining the experimental design in the Differential Expression for RNA-Seq tool, and can be used to add extra layers of insight in the Create Heat Map and PCA for RNA-Seq tools. To learn more about how to create a metadata table, how to import a metadata table, or how to associate data elements with metadata, see

In the next step, the parameters for the Pathway Analysis tool need to be set. Setting the parameters in a workflow context is not as user-friendly as when run stand-alone, because the parameters from the different pages are grouped on the same page in workflow execution. To help clarify this, it is indicated in figure 4.10 which parameters pertain to the IPA upload, and which pertain to the IPA analysis.

Image ipawf_step3
Figure 4.10: Selecting the Pathway Analysis tool parameters for upload to IPA and analysis in IPA.

In the final step, standard result handling is performed: The selected parameters can be previewed, and an output location must be chosen.