[BioC] Microarray: correlation and Rgraphviz

[Martin Morgan]

On 02/04/2012 10:38 AM, CAM HABI wrote:
> Dear all,
>
> I'm a basic R user and would be very grateful for some help.
> I have a filtered gene list of 1500 Affy probesets and run a simple correlation. Following a correlation threshold, I try to plot the graph using Rgraphviz. However, all 1500 probesets are plotted. How can I plot only those probesets that are correlated according to the set threshold, i.e. only those with an edge?
>
> Many thanks for your help!
>
> Cam
>
>
> cor = cor(t(list))
> diag(cor) = 0
> selcor = abs(cor)>0.9

subset the matrix here, e.g., selcor[rowSums(selcor) > 0, 
colSums(selcor) > 0]. Martin

>
> graph = as(selcor, Class = "graphNEL")
> plot(graph, "neato")
> 	[[alternative HTML version deleted]]
>
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