[BioC] Dye swap time course experiment in marrayinput

[Naomi Altman]

For normalization the batches of slides do not matter if you use the usual 
2-color normalization methods, which normalize each slide separately.  If 
you want to do multi-array normalization, you need to read all the arrays 
into a single batch.

However, for analysis, you likely want to use some type of ANOVA.  For 
this,  it is more convenient to read in all of the arrays in a single batch.



At 09:18 AM 1/23/2004, Richard Friedman wrote:
>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".
>-Rose Friedman, age 7
>(These are the correct lyrics and supersede
>the version previously at the end of my sig)
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111