I am currently doing my masters project about cardiac diseases.
So we took 14 patients and did rna seq and we got our results as FPKM. I will be using IPA software to create networks and pathways etc..
so my questions are :
What values of fpkm are considered to be significant ?
We have no control , so we will be taking patient 13 as the control beacause he has the least severe phenotype so how can I compare all patients fpkm to patient 13 ?(to know what genes are up/down regulated) I did a ratio between every fpkm for every gene is it correct ?
What cut-off should i consider ?
Results are in excel form as either expression profile g and expression profile G so whats the difference and which one should I take ?