I am new to R want to know that I have already normalized data for lncRNA and mrna means Excel files for different regions for Male and female I want to first find out lncrna mrna interaction and build network and then compare 1.I want to find out pearson correlation for each pair of lncRNA and mRNA (Note:Two lists are not equal) How can I find out pair wise corealtion ??? I have to compare each each and every mRNA against each of lncRNA? Second point is do I need their attribute to compare like FC or Exp Value or just name list for both of them is enough? ;
Your title has answer.
Use WGCNA to find the co-expressed lnRNAs and mRNAs. If you have enough sample size ( min. 20 samples recommended ), you could run WGCNA and identify the tightly co-expressed LncRNAs and mRNAs.
WGCNA had pretty detailed documentation and several lectures on youtube from the author.