[BioC] Extracting top upregulated genes from Limma analysis

[Iain Gallagher]

tops <- topTable(fit2, number=Inf) # get all genes
tops[which(tops$logFC > 0), ] [1:50,] # up reg top 50
tops[which(top$logFC < 0), ] [1:50,] # down reg top 50

best 

i

--- On Wed, 2/3/11, Casper Shyr <casshyr at hotmail.com> wrote:
tops <- topTable(fit2, number=Inf) 
> From: Casper Shyr <casshyr at hotmail.com>
> Subject: [BioC] Extracting top upregulated genes from Limma analysis
> To: bioconductor at r-project.org
> Date: Wednesday, 2 March, 2011, 5:41
> 
> Hello,
>   I have my results after running a microarray
> analysis. In general, the analysis is basically comparing
> gene expressions in 1 tumor group to another.
>   Below are my relevant codes:
> 
> mm2 <- model.matrix(~TumorType, pData(eset2))
> fit2 <- lmFit(eset2, mm2)
> fit2 <- eBayes(fit2)
> 
>   Now I want to extract the top 50 up-regulated genes,
> but I am not sure how to do so. I know with toptable
> function, I can extract the top differentially expressed
> genes, but what if I only want the up-regulated ones? 
> 
>  Thanks in advance!
> Sincerely,
> Casper
>     
>         
>           
>   
>     [[alternative HTML version deleted]]
> 
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