[BioC] Bayesian method in limma

Gordon Smyth smyth at wehi.edu.au
Tue Jul 20 02:21:33 CEST 2004

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.


>I highly appreciate your help.
>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

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