Question: Taking out Heatmap cluster from heatmaply
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gravatar for krushnach80
19 months ago by
krushnach80470
krushnach80470 wrote:

I plotted this correaltion heatmap using heatmaply i m getting cluster that forms good correlation. Is there any way i can take out the gene pairs or set of genes that are forming high correlation.

Second approach

I m making a correlation matrix . So is there a way to take out set of genes that are giving a good correlation.Such as if i set a threshold of lets say 0.6, is the threshold , how do i filter those genes. Any suggestion or help ,if i can do that in R?that would be helpful

heatmap

R • 902 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by krushnach80470

What kind of down-stream analysis are you planning? What do you mean by 'take out', keep or filter, or remove redundant features for feature selection? If feature selection, there is a recipe here: http://machinelearningmastery.com/feature-selection-with-the-caret-r-package/ using the caret R package.

ADD REPLYlink written 19 months ago by Michael Dondrup45k

I would look for pathway with the genes that are showing really good correlation.
"What do you mean by 'take out', keep or filter, or remove redundant features for feature selection? " I meant that if there is a good correlation how do i take those set of genes and values?

ADD REPLYlink written 19 months ago by krushnach80470

What about your earlier question: Saving individual clusters from heatmaps which has a validated answer? please explain what is different with your new question.

ADD REPLYlink written 19 months ago by Michael Dondrup45k

I did that with complex-heatmap i took out clusters but i'm not sure if those clusters are highly correlated ,i did define cluster that the km parameter .So im not sure if those are highly correlated or not. So if they are forming a cluster then they are correlated ?

ADD REPLYlink written 19 months ago by krushnach80470
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