Hello,

you can just sort the topTable result by the t-statistics since these  
will be either positive or negative, or call it directly with  
sort.by="t" and then filter for significant p-values.

HTH
\Heidi

On 15 Sep 2009, at 10:05, zrl wrote:

> Dear List,
>
> I have several biological replicates affy arrayes (a simple one  
> group 4
> arrayes), and tried to use eBayes to get the differentially  
> expressed genes.
> The topTable ranked the genes by B statistics, which mixed over- 
> expressed
> genes and under-expressed genes. My question is how I should  
> separate the
> over and under expressed genes from topTable results. My idea is to
> calculate the mean average expressed value/intensities (extracted from
> topTable results with using the number of all the genes) and  
> compare ranked
> genes with the mean value, if the expressed value is greater than  
> the mean,
> I take this gene as over-expressed, otherwise, it's under-expressed.
> Since I don't know the underlying implement of topTable or eBayes,  
> I want to
> make sure if my method is right. Or you have some better ideas.  
> Thanks.
>
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