I have RNA-seq data. I performed differential analysis between Tumor and Normal samples for coding and lncRNAs separately. I have 1300 differentially expressed coding genes and 140 differentially expressed lncRNAs after differential analysis with DESeq2.
I want to identify the function of lncRNAs and for that I want to construct Co-expression network between coding and lncRNAs.
I have seen some packages like WGCNA and Cemitool for Co-expression network. But I have few questions.
1) For Co-expression network Should I use all the coding and lncRNAs as input (OR) only differentially expressed coding and lncRNAs?
2) Input should be counts data or normalised counts?
Any help is appreciated.