[BioC] maNorm 2D

Floor Stam fjstam at bio.vu.nl
Tue May 11 16:48:27 CEST 2004

Hi Matthew

tRMA (http://www.cmis.csiro.au/iap/tRMA/docs/tRMA.pdf) also has a 
spatial-normalisation function, this one is described in a paper by 
Wilson et al. in Bioinformatics (june 2003). It is better documented 
and, in fact, the only one that worked for me since the 2Dloess 
function in the maNorm package produced M values that varied around -50 
instead of 0.


Floor Stam

Vrije Universiteit Amsterdam
Faculty of Earth and Life Sciences
Department of Molecular and Cellular Neurobiology
De Boelelaan 1085
1081HV Amsterdam
The Netherlands

Ph: 	+31-20-4447114
Fax: 	+31-20-4447112
e-mail: fjstam at bio.vu.nl
On 10 May 2004 , at 18:55, Matthew Fero wrote:

> 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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