find the co-expressed gene with genes of interest in ngs data

Question

[deepakkarthik02]

Hi all,

I wanted to find the genes that are co-expressed with my set of genes of interest. So I used genefilter package . In my data, column name is patient id and row name is gene name (the data is normalized rnaseq data from tcga). I am able to read the data in matrix and loading to the function gene finder. But it is not bale to give out the names of genes. Can any one please correct me or can you please suggest me a better package?

Thank you

karthik

Answer 1

[Michael]

If you follow the documentation, you can easily see how gene names can be derived. If that doesn't work for you, you are maybe doing something wrong, be we can't guess what. So please provide a reproducible example next time.

Answer 2

[EagleEye]

This would be the easiest solution to your problem: Gene co-expression analysis