I am looking into co-expression analysis of genes at different developmental stages. I am stuck up with few things. I would be grateful if you could help me out.
Basically I want to find genes coexpressed to a set of bait genes in different stages and genes co-expressed in particular stage too. So I thought I should do DEG analysis between stages and co-expression analysis for all stages and then I can get uniquely coexpressed genes in one stage. So I need to do DEG and coexpression. I am using publicly available RNA-SEQ data.
In one dataset I have genes, FPKM values, their annotations and the trinity assembly(fasta). But, I found that using FPKM values for DEG or co-expression analysis is not recommended and I neither can give it as input to existing softwares. So I do not figure out what can I do here.
In the second dataset, I have logCPM values obtained from (limma,voom:Reference-manuscript methods) of genes across different stages. They range from -5 to 12. How do I find DEG with this? Can I directly use them to take cutoff and what cutoff? Cause I do not have any other details.
Thanks in advance!