Toolbox | Transcriptomics Analysis ()| Annotation Test | Hypergeometric Tests on Annotations ()
This will show a dialog where you can select the two experiments - the larger experiment, e.g. the original experiment including the full list of features - and a sub-experiment (see how to create a sub-experiment in Creating sub-experiment from selection).
Click Next. This will display the dialog shown in figure 27.95.
At the top, you select which annotation to use for testing. You can select from all the annotations available on the experiment, but it is of course only a few that are biologically relevant. Once you have selected an annotation, you will see the number of features carrying this annotation below.
Annotations are typically given at the gene level. Often a gene is represented by more than one feature in an experiment. If this is not taken into account it may lead to a biased result. The standard way to deal with this is to reduce the set of features considered, so that each gene is represented only once. In the next step, Remove duplicates, you can choose how you want this to be done:
- Using gene identifier.
- Keep feature with:
- Highest IQR. The feature with the highest interquartile range (IQR) is kept.
- Highest value. The feature with the highest expression value is kept.
At the bottom, you can select which values to analyze (see Selecting transformed and normalized values for analysis).
Click Next if you wish to adjust how to handle the results. If not, click Finish.