[base] loop designs and duplicate annotations

[Boer, T.E. d. <te....@vu...>]

Hello

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