[BioC] Factorial experiment combined with blocking designs

[Wu, Xiwei]

Dear BioC members,
 
I have a general question on analysis of complicated designed microarray
experiment.The experiment is designed as follows:
 
Factors interested:
1. Cell Type: WT, MU1, MU2, MU3
2. Treatment: Hormone and Untreated
Each combination of treatment was repeated twice and hybridized to Affy
genechip.
 
Because the experiment is time-consuming, two technicians will do the
experiments at two different time.
Extraneous factors not interested:
1. Day: two lelves
2. Experimenter: two levels
 
Correct me if I am wrong: If the experimter and day is combined, it is a
randomized block design. Otherwise, it will be a latin square deisgn. 
 
We are only interested in the cell type difference and treatment difference
or their interaction, but not day or technician effect. I think this
situation could be quite common in practice. My question is :
1) Is there a package helping design such experiment? 
2) Is there a way to analyze the data using Limma packages or other R
packages?
 
Any input will be highly appreciated,
 
Xiwei Wu, MD, PhD 
Assistant Research Scientist
Department of Biomedical Informatics
Beckman Research Insitute
City of Hope National Medical Center
Duarte, CA 91010
Phone: (626) 359-8111 ext. 65071
 
 
 
 

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