Hi Daniel,
MapMan can perfectly visualize your data - the problem is that you have accidentally chosen
the mapping file for the ATH1 array. Please choose the mapping called Ath_AGI_ISOFORM_MODEL_TAIR10_Aug2012
from the list of mappings in the tree view on the left half of the MapMan main window. If this mapping
file is not listed there, you can download it directly fron within MapMan by right-clicking on "mappings"
in the tree view and then choosing "new mapping"->"download". A dialog box listing all available mappings
will pop up and you can select the mappings you would like to obtain.
I hope this solves your problem.
BTW: When working with RNA-Seq data you might find RobiNA (another tool we develop) quite
useful for quality checking, filtering and statistically assessing differential gene expression.
Visit:
http://mapman.gabipd.org/web/guest/robin cheers,
Marc