Question: query regarding miRNA-mRNA co-expression analysis
0
gravatar for Thind
9 weeks ago by
Thind70
Thind70 wrote:

I am trying to integrate expression data of miRNA-mRNA (~20 samples). I have a few queries such as which one is the best method for co-expression calculation (my interest is anticorrelation) 'Pearson', 'spearman','Kendall', 'Mutual information' etc? and why?

My aim is to extract miRNA-mRNA pairs with anticorrelation <-0.3 with statistical significance and further mapped those pairs with different databases which contains interactions either predicted or experimentally validated. One R Package Anamir seems to have these functionalities but it misses the significance part (p-value of the correlations).

I did above part by my own, however, I am sure what is the best input for calculation of correlation; eg, the log transformation of raw values or cpm value or other normalized expression values?

It would be great if anyone knows any good package or this kind of analysis or can explain some of my queries.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Thind70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2018 users visited in the last hour