Hi, I have some CEL files that I would like to analyse with R. I managed to import them and to add the experiment description adding a covdesc file to my directory (I have two groups that I want to compare). Unfortunately I cannot continue to work with Affy because my Clariom S Mouse Background is not supported by Affy. How do I manage to add my experimental description using oligo? Is there any way to make it work using Affy? Thanks a lot!

The oligo package works almost identically to the affy package. And all of the objects for oligo are variants of the ExpressionSet objects that affy used, so doing what you think you should do will tend to work the same. And there is a vignette you can read.