[BioC] hierarchical clustering data after LIMMA - agilent two color

[David Ruau]

Adrian,

Starting from your list of significant genes:
:> library(simpleaffy)
:> library(bioDist)
:> pdf(file="heatmap.pdf",height=8, width=8)
:> heatmap(exprs(data.rma)[my.list,], col=blue.white.red.cols,  
distfun=euc, hclustfun=function(c){hclust(c,method='average')})
:> dev.off()

David

On Apr 1, 2008, at 2:44 AM, Adrian Johnson wrote:
> dear list:
>
> I finished a LIMMA analysis for two color Agilent 4x44 arrays. I  
> found 800
> genes (my choice of fold change under -2 and over +2) at 5%FDR.
>
> I have 30 normal(cy3) and cancer (cy5) samples (paired design).
>
> how can I do clustering and make heatmap after getting significant  
> genes
> (eBayes(lmfit) step).
>
> Appreciate your help.  thanks
> Ad.
>
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