I have recently installed and started using BASE for our microarray data and I 
am at the moment importing already existing data into the database. We use 
custom two color Agilent microarrays and our experiments often use loop designs 
instead of reference designs. Using a loop design means that for most 
microarrays both labeled extracts are important for the analysis (since both 
contain exposure data instead of one being exposure data set against a 
reference sample). Because of this, raw bioassays have to inherit annotations 
from both extracts but when I design experiments I get errors and warnings 
about duplicate annotations. Is there a way that BASE can deal with dual color 
data where annotations have to be used for both color channels and if so how is 
this done?

Thanks in advance and kind regards
Tjalf de Boer
VU University Amsterdam
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