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.
"How to build a graph" and you mention 4 different languages? Try to pick a single language and specify what kind of graph.
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:
See igraph documentation if you want to convert it to R graph object:
source this file and use
myDendrogram <- dendrogramSamples(yourData)
I need a graph with nodes as gene names and edges as significant correlations, not dendrogram, but THANKS, FOLKS
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