[R] co-expression network of coding-noncoding genes

[Elham -]

hello all,

I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq analysis by CLC genomics,after normalization I calculated correlation, I have many pairs of coding and lncoding molecules that correlate according to their expression,I filtered them (> 0.9 and < -0.9). Additionally, I've considered the pairs that have p-values < 0.001,but they are many pairs yet.

now for more filtering I want to consider the pairs of coding-non coding, which are both deferentially expressed. 
how can I have DE for all treated vs all controls samples for coding and DE for all treated vs all controls samples for noncoding?


I should say that each experiment is effect of one drug on one cancer (drugs and cancers are different in each experiment ) but the platform is similar and all of them are Illumina HiSeq 2000 (Homo sapiens)

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