Clustering of gene co-expression network using igraph R package

Question

[aiswaryabioinfo]

I have a gene co-expression network obtained from RNA-seq data which has more than 10000 nodes and more than 10 lakh edges. I need to cluster this network. Can anyone please suggest a method to cluster this effectively.

I tried with igraph R package, in igraph package many clustering methods are there. How can I identify which is the appropriate method for large gene co-expression network.

[Kevin Blighe]

May help - Network plot from expression data in R using igraph ?

[aiswaryabioinfo]

Thank you for the guidance

Answer 1

[Jean-Karim Heriche]

There's no right answer to the question of which clustering method is appropriate. You need first to define what appropriate is in your context and second, how you are going to evaluate the outcome. With clustering one may need to explore different approaches as outcome is dependent on what structure is present in the data and on what one expects/wants to see (subject to other constraints such as being able to compute when the data is big).