I am doing gene expression profiling of 3 structures(A,B,C). I compared (A vs B&C), (B vs A&C), (C vs A&B). I found 1, 2 and 20 DEG respectively between groups comparison. Are there any problems with these results, do I need to remove non-coding RNA before DEG analysis? I tries to find document and script to do so but I couldn't find one. Can you help me solving these problems?
Thanks for your comment, could you tell me the function to remove non-coding gene ?