criteria for pvOutputThreshold = 1e-100 in EQTLMATRIX and creation of geneloc.txt for ciseQTL

Question

[Nai]

I would like to know the following points in MATRIXEQTL:

(i) what is good threshold value for pvOutputThreshold = 1e-5 / 1e-6 / 1e-100 in MATRIXeQTL ? (ii). Best model for eQTL Linear/cross_linear/Anova when I don't have co-variate information? (iii) MATRIXEQTL needs geneloc.txt (Gene Name, Chr, s1 , s2), I understood about snploc.txt. (iv) How can visualize eQTL for specific genes, visualization of all eQTL