[BioC] Bayesian method in limma

[Hua Weng]

Dear Gordon:

I tried to use ebayes() method to pick differential expressed genes for our
two color cDNA microarray data analysis. Our expreiment is designed to
anaylysis the influense of one chemical on cotton genes. It is a
Single-Sample Expreiment and two RNA sources are comapred deirectly on 3
biological replicates through time course. But we don't have complete cotton
gene library. So we hand pick around 200 genes that we expect to be
differentiall expressed and print them 12 times (technical replicates) on
the same slide. I have following questions:

(1) Based our expreiment design, is it still suitable to use ebayes() method
to pick differentially expressed genes for our data?

(2)I took a look at help file for ebayes() and found out the default vale
for proportion is 0.01. What value should I set for proportion for our case?
Do I need to change default value for stdev.coef.lim?

I highly appreciate your help.

Hua

Microarray Core Facility
Department of Biochemistry and Molecular Biology

Oklahoma State University

348E Noble Research Center

Stillwater, OK  74078

 Phone:  405-744-6209

Fax:    405-744-7799