How about using the older function:



ord <- order(fit$lods,decreasing=TRUE)

top50 <- ord[1:50]

plot(x=fit$coef, y=fit$lods,cex=0.4)

points(fit$coef[top50],fitb$lods[top50],col="red",cex=0.4)



hope it helps

Giovanni







On Nov 8, 2005, at 3:49 AM, Gordon K Smyth wrote:

> [Moved from Bioc-devel]
>
>> Date: Mon,  7 Nov 2005 09:32:39 -0600
>> From: Edoardo Giacopuzzi <gedoardo@bluebottle.com>
>> Subject: [Bioc-devel] Draw volcanoplot in Limma
>> To: bioc-devel@stat.math.ethz.ch
>>
>> Hi, I'm using from little time to analyze my microarray data.
>> After using eBayes() function to compute the odds ratio for my genes
>> now i want to draw a volcano plot showing my data.
>> I've used the volcanoplot() function as follow:
>>
>>> volcanoplot(fitNorm, highlight=500, names=fitNorm$genes$ID)
>>
>> and I get a volcano plot with 500 gene highlighted, each one with his
>> name... So the resulting graph is quite confused!
>>
>> I want to know if there is a way to obtain a volcano plot with dots
>> rapresenting my top-500 genes designed, for example, in a different
>> color (but without names labels).
>>
>> Thanks!
>> Edo
>
> Dear Edo,
>
> No there's no way to highlight points in a volcanoplot without  
> labels, although there probably
> should be because, as you say, a large number of labels is quite  
> confusing.
>
> Note that I've moved this thread to the bioconductor mailing list.   
> (You've sent three limma
> questions now to three different lists.  Seriously, only the  
> Bioconductor list is appropriate for
> queries about using Bioconductor packages.)
>
> Best wishes
> Gordon
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


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