[BioC] Experimental design for mutiple groups of paired samples

[Wu, Xiwei]

Dear list,

I have eight samples with following structure:

Control input
Control enriched
Treatment A input
Treatment A enriched
Treatment B input
Treatment B enriched
Treatment C input
Treatment C enriched

Note that each input is paired with an enriched sample. These are
chromatin immunoprecipitation samples. My interest is to compare the
different enrichment between each of the treated samples and controls. I
am also potentially interested in enrichment differences among A, B and
C. I have to use two-colored array due to experimental nature. Assuming
that obtaining enough biological replicated samples is not an issue,
what is the best hybridization approach? I am thinking about hybridizing
each of the enriched sample vs. its control, and then using a loop
design (which needs 4 arrays, or a saturated design which needs 6
arrays) to connect all the enriched samples. I am not sure whether that
is a good approach.

Any suggestion will be highly appreciated,

XiweiXiwei Wu, MD, PhD 
Director, Affymetrix and Data Analysis Core Facility
Assistant Research Scientist
Department of Biomedical Informatics
Beckman Research Institute
City of Hope National Medical Center
Duarte, CA 91010
Phone: (626) 359-8111 ext. 65071

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