[simonandrews]

Okay thank you very very much !
However I just realized the quantitation for each probe is not what I was expecting. In fact I see for example that one probe houses 8 reads (no duplicates), but the displayed value is 6,383.
(and the only quantitation I ran is the "read count quantitation" which should give me a value of 8 for this probe if I understand correctly)

Without seeing what options you used for the quantitation it's difficult to know why you didn't get the value you expected.

Assuming you have a normal, unspliced library and that you really want raw counts then you would indeed use the read count quantitation, but you'll need to turn off the option to correct for total count and the option to log transform the counts. You should then get the counts you expect.

If you still can't make it work then can you make up a probe list description report (Reports > Probe List Description Report) from your All Probes list and email it to me. If you could also send me a view of the chromosome view for one of the features you think is incorrectly quantitated I can try to figure out what's going on in your case.