Dear Bioconductor group.

	I have 2 questions on Normalzation with LIMMAGUI

1. When LimmaGUI exports normalized m-laues values is it always
as log(Cy5/Cy3)?

For example with the following target file for a dye reversal 
experiment:

SlideNumber FileName Cy3 Cy5 Date

18370n_13430283.spot Ndigest Nundigest  10/3/06
28370n_13430572.spot Nundigest  Ndigest 10/3/06
38370t_13469544.spot  Tdigest Tundigest10/17/06
48370t_13469546.spot  TundigestTdigest 10/17/06


Would the data for 28370n_13430572.spot have to be multiplied by -1
  in order to be compared with the date for 18370n_13430283.spot?


2.  After one normalizes data with LimmaGUI using Normalize/ Update M 
and A,
and then specifies the same normalization conditions when computing the 
linear model,
does this result in the normalization being applied to the data
once or  twice? And if twice would it yield different results  over 
normalizing the data once?

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"My novel has a hundred characters and it takes place over a year.
When I finish it, if it is shorter than Ulysses, then Joyce described 
things
too much".
-Rose Friedman, age 9
	[[alternative text/enriched version deleted]]

