reproduce the IBD case study, permutation p value is very bad

[yiluheihei]

I reproduced the IBD case study, and the empirical p value is very bad (close to 1). Did something go wrong?

My code is as following:

mSet<-InitDataObjects("pktable", "stat", FALSE)
mSet<-Read.TextData(mSet, "iHMP2_48_metaboanalyst_input.csv", "colu", "disc");
mSet<-SanityCheckData(mSet)
mSet<-ReplaceMin(mSet);
mSet<-PreparePrenormData(mSet)
mSet<-Normalization(mSet, "MedianNorm", "LogNorm", "AutoNorm", ratio=FALSE, ratioNum=20)
mSet<-PLSR.Anal(mSet, reg=TRUE)
mSet<-PLSDA.CV(mSet, "T",5, "Q2")
mSet<-PlotPLS.Classification(mSet, "pls_cv_0_", "png", 72, width=NA)
mSet<-PlotPLS.Imp(mSet, "pls_imp_0_", "png", 72, width=NA, "vip", "Comp. 1", 15,FALSE)
mSet<-PLSDA.Permut(mSet, 1000, "accu")

Thanks for your attention.