Hi 
I've done PCA for my gene expression data after DEG analysis, I can see that my case and control samples clustered distinctly but **I want to report a p.value for this result**, it worth to notice that I have the coordinate csv file that represents coordinates of samples from different phenotypes (case vs control).

Thanks in advance
PCA is an exploratory data analysis method. It does not test a null hypothesis and generate a p-value. 

If you want to compute a p-value maybe you should try pvclust package in R. It didn't use PCA but a hierarchical clustering and report p-values for each sub-tree

http://stat.sys.i.kyoto-u.ac.jp/prog/pvclust/