Microarray: correlation and Rgraphviz
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CAM HABI ▴ 10
@cam-habi-5093
Last seen 7.1 years ago
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 graph = as(selcor, Class = "graphNEL") plot(graph, "neato") [[alternative HTML version deleted]]
affy Rgraphviz affy Rgraphviz • 693 views
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@martin-morgan-1513
Last seen 10 weeks ago
United States
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793