I know I know I know that my question may seem silly to you. And I know I'm not as professional as you are, but please note that I HAVE RESEARCHED TO FIND THE BEST ANSWER, but I don't know if my keywords weren't appropriate because the more I searched on google and specifically on biostars, the more I feel confused.
I have a list of P-values, Log2FoldChanges and Standard Deviations (SD) of Log2FoldChanges for each gene in a time-course RNA-seq study. I'm going to find the DE genes based on the info I have been provided. According to my researches, some say that we should use the adjusted p-values to find the DEG, which means I should use the command "p.adjust" in R to adjust my current p-values. But I have also seen that some people use FDR and FC. On the other hand, everyone recommends a different criteria to find DEG. One says, "find DEG with adjusted p-values<0.1". Another one recommends using adjusted p-values<0.05.
I'm getting confused that,
1- which one is the best solution to find DEG? P-values, adjusted p-values, FDR, FC? I'm not sure whether FDR and FC could be used to find DEG. I just repeat what I have read.
2- whatever you recommend me in question number 1, what criteria do you recommend? 0.05? 0.1? etc.
3- if P-value (or its adjusted value) is enough, what is log2FoldChange and its SD good for? why is it provided beside P-values by the package I'm using?
I apologize if my question is so basic and may bother you. And thanks for your help.