How to normalize the RNA seq data for the purpose of correlation analysis

[bioinfor]

For the purpose of finding differentially expressed genes, there are methods such as DEseq and cuffdiff. It was said that DEseq is better choice for this purpose.

Now I am going to do correlation analysis using RNA seq data, to find gene pairs that significantly correlate with each other. For this purpose, I wonder whether I can use the pre-processed and normalized results from DEseq or cuffdiff ? Actually, I want to do the correlation analysis between miRNA and mRNA based on RNA seq data.
Does anyone have any idea about this?
Thanks.