I have 3 High-throughput RNA-Seq samples from patients with rare disease and 3 samples from healthy subjects. I have identified the differentially expressed lncRNA and coding-genes between patients and control subjects. I would like to predict the function of identified differentially expressed lncRNA based on the expression of coding genes. What is the best method for this goal ?
I found that one way is to calculate the Pearson's correlation coefficient (PCC) between the expression values of each of the lncRNA-mRNA pairs.
I would like to know is this approach valid for my sample size ( 3 patients) ?
Should I just calculate the Pearson correlation confidence base between the expression values of each of the lncRNA-mRNA pairs only across patients samples?