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How to build a graph from the microarray gene expression values using correlation functions?
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5.6 years ago
Belarus

How to build a graph from the microarray gene expression values using correlation functions? I need a tutorial in R language and Python/Ruby/Java. I tried to use ReactomeFI and a recipe from R bioinformatics cookbook.

Thank you

R gene • 2.3k views
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"How to build a graph" and you mention 4 different languages? Try to pick a single language and specify what kind of graph.

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20 months ago
Canada

I imagine you want a weighted graph based on correlation coefficients.

If your rows are gene names, you can simply do :

my_microarray_mat = as.matrix(whatever_data_frame_I_loaded_my_file_into)

my_cor_mat = cor(t(my_microarray_mat),method = "pearson")

method is by default pearson and you can change it to anything. Type:

?cor

See igraph documentation if you want to convert it to R graph object:

http://igraph.org/r/

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19 months ago
Irsan ♦ 6.9k
Amsterdam

source this file and use

myDendrogram <- dendrogramSamples(yourData)

plot(myDendrogram)
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I need a graph with nodes as gene names and edges as significant correlations, not dendrogram, but THANKS, FOLKS

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