[BioC] maNorm 2D

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Mon May 10 19:16:51 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?

Yes.  In general in the S formula language * represents an interaction
term (actually main effects and interaction), not arithmetic multiplication.
See the R documentation for formula, and for loess.

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