Hi all,

I have some data (10 arrays with ~25000 features each, hybed in a loop
design) that I wanted to background correct because of apparent
non-linearities observed in MA plots. After applying a kooperberg
correction, I replotted the data and noticed that while the overall set was
much "tighter" and more linear than before correction, a new artifact
appeared in the plots. Namely, rather than all plotting on a horizontal
line, the data took the shape of the open jaw of a shark, with the upper jaw
horizontal as it should be but a lower jaw of data sloping downward from the
horizonal at a 45 degree angle.  This was all lower intensity data that
plotted in the under 10 log-units region of the MA plot. I tried simple
background subtraction, but this did not eliminate the non-linearities I
originally observed.

I dont' really understand this message as these were nice hybs with
backgrounds around 100-150 RFU, average signals around 4000RFU and no
notable irregularities. Can anyone advise me?

Thanks in advance of your reply,

Matt

-- 
Matt Scholz
Senior Research Specialist
Department of Plant Sciences
University of Arizona
(520) 621-1695

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