On 9/9/05, Henrik Bengtsson <hb@maths.lth.se> wrote:
> 
> A.J. Rossini wrote:
> > Interesting -- does anyone know if you need to "compensate" for 4-color? 
> (I
> > know that you _sometimes_ have to for 4-color flow cytometry)
> >
> > best,
> > -tony
> 
> Most likely, yes! Use affine normalization to do it. It works for two
> or more channels. I've got all methods implemented in aroma (search
> google), but I'm about to release a lightweight version of this called
> aroma.light. For the moment see the below tech report (another version
> submitted) at http://www.maths.lth.se/bioinformatics/publications/:
> 
> H. Bengtsson and O. Hössjer, Methodological study of affine
> transformations of gene expression data with proposed normalization
> method, Preprints in Mathematical Sciences 2003:38, Mathematical
> Statistics, Lund University, 2003.
> 
> Quantile normalization a la RMA (Affy) would also do, but has more
> degrees of freedom compared to the 2*nbrOfChannels-1 parameters for
> affine normalization.
> 
> 
> 
> Henrik
> 
> PS. I'm going to MGED in Norway soon, so I'll be online less often. DS.
> 
> 
Well, what I was suggesting was based on selection of dyes. With 4-color 
flow cytometry data, if the colors are not well selected, you have to worry 
about "bleed-over", so bad (or "forced by manufacturer") selections require 
that you may have to compensate (down-grade) for bleed over from the other 
channels if the wavelengths of the colors are too close or the selectivity 
is too wide.

It's definitely true for 8-color and higher flow data, borderline for 4/6 
color.

-- 
best,
-tony

blindglobe@gmail.com
Muttenz, Switzerland.
"Commit early,commit often, and commit in a repository from which we can 
easily
roll-back your mistakes" (AJR, 4Jan05).

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