[BioC] Dye swap time course experiment in marrayinput

[Richard Friedman]

Dear Bioconductor Users,

	I have a time course experiment using a dye swap There are 18 slides 
in all, and a tiff file
for each slide.The  slides may be described as

condition1cy3-condition2cy5 time1	3 slides  6 tiff files
condition1cy5-condition2cy3 time1 3 slides  6 tiff files
condition1cy3-condition2cy5 time2 3 slides  6 tiff files
condition1cy5-condition2cy3 time2 3 slides  6 tiff files
condition1cy3-condition2cy5 time3 3 slides  6 tiff files
condition1cy5-condition2cy3 time3 3 slides  6 tiff files

My question: In marrayinput, when I read in the files, preparatory to 
normalization,
I have to use a file analogous to SwirlSample.txt in the example.  In 
that file, do
I read in:

1. All 18 slides.
or
2. Just the 6 slides from the first time point, so that the slides from 
the other 2 time points
should be read in and normalized in separate runs.

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 at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"Spring, Summer, and Winter.
Then Fall came along,
and that's the end of our song,
and the pigeons never hibernate at all".
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