[BioC] Bayesian method in limma

[Gordon Smyth]

At 01:42 AM 20/07/2004, Hua Weng wrote:
>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?

You can still use ebayes(), but use the moderated t-statistic rather than 
the log-odds (B-statistic) because the former doesn't require an estimate 
of the proportion of differentially expressed genes.

A more subtle question is to normalize data where most or all of the genes 
are differentially expressed.

Gordon

>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