[BioC] RG-to-MA transformation in protein arrays

[Saroj Mohapatra]

Hi all,

I have a basic question (perhaps too basic!) regarding RG to MA
transformation. I understand the logic of the MA transformation as
described by Terry Speed and other documents. 

My situation is a bit different from cDNA arrays. In this case, the red
intensity refers to variable reactivity of a sample (hopefully,
containing antibodies) against known antigens on the chip (each spot has
different antigens). The green channel refers to reactivity against a
constant protein (each spot has the same one) that is arrayed for the
purpose of checking against variable protein deposit because of
print-tip variation, day-to-day variation of the way in which the
proteins are prepared, etc. The green intensity across the spots is
never constant within a chip, indicating the variations as mentioned
above.

Therefore I think that the ratio of even a very reactive spot in the
chip might or might not achieve a red:green ratio of 1. I wonder, if it
has any impact on the issue of RG-to-MA transformation?

M = log2(R/G) makes perfect sense to me, but I am not able to understand
the significance of A = 1/2(log2(R.G)) in this case. Any pointers would
be helpful.

Thanks and regards

Saroj Mohapatra

---------------------
Saroj K Mohapatra, MD
Research Associate
Karmanos Cancer Institute
Wayne State University School of Medicine
110 E. Warren, Room 311
Detroit MI 48201
313-833-0715 x2424
saroj at wayne.edu