[BioC] maNorm 2D

Matthew Fero mfero at fhcrc.org
Mon May 10 18:55:27 CEST 2004

I'm having difficulty understanding the "twoD" option of the maNorm 
function.  It seems like the idea is to normalize for two-dimensional 
spatial artifacts on the cDNA array.   Is this correct?   Looking at 
the source code the relevant function would seem to be:
loess(z ~ x * y, weights=w, .....
where z = maM values, x = row locations, y = column locations.
What I don't understand is how maM values can be normalized relative to 
the mathematical product of row and column locations (x*y).   This 
would not seem to be a 2D representation of location, e.g. location 
(7,3) = (3,7).   Does the "*" operator have some other meaning here?

A second question is whether it is possible to perform 2D loess across 
an entire array as opposed to within a print-tip group, and whether it 
is possible to perform normalization based on 2D background 
measurements instead of foreground measurements?

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