Hi Sergio,
It is possible to create groups such as before and after treatment. For that the samples that are before treatment have to be distinguished from samples that are after treatment.
It is possible to add a flag to the SAMPLE data file, to differentiate which is before and which is after. Then it is possible to use that flag to filter samples and create separate groups.
If that is not possible, then add all samples that are before treatment using Custom Selection as shown in the image below. Then create a group based on that list of Sample IDs. Add all the samples that are after treatment and created another group.
Then group comparison can be done between Samples before and Samples after treatment.
Hope this helps.
thanks
Jag