i am very new to this field, so please bear with me. I have 600 parameters, on which i perform simple pairwise x,y correlations.For adjustment of the p-values ive been stuck between two R-packages.
FDR-tool gives me a set of qvalues,
FDR <- fdrtool(as.vector(a$P[!is.na(a)]), statistic=c("pvalue"), cutoff.method=c("fndr"))
whereas the p.adjust command in the basic packages gives me adjusted p-values.
FDR <- p.adjust(as.vector(a$P), method = "fdr", n = length(as.vector(a$P)))
"a" is an object created by the hcorr command of the package "Hmisc"
The output is not the same, however.
Can someone please explain me why that is? And how to proceed from here? I was told, the adjusted p-values (as obtained from p.adjust) can be treated as such, that i can just define a cutoff of 0.05 for false positives. I am not so sure about q-values, though, and if i am missing something fundamental on False Discovery Rates. Thank you very much!