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Reputation: 395

Welch t-test, adjust p-value on permutation based FDR in R

I would need some help to find a way to compute q-values from Welch p-values in R, using permutation FDR method, as for SAM technique.

Assuming my data are as follow

x = matrix(rnorm(1000*3),nrow=1000)
y = matrix(rnorm(1000*3),nrow=1000)

I can obtain a list of Welch p-values for each 'row x-vs-y' as follow

pvalues = sapply(1:1000, function(n) t.test(x[n,], y[n,])$p.val)

How can I then adjust the p-values using permutation fdr? As far as I can see, p.adjust cannot do this, samr allows only t-statistic or wilcoxon and, I cannot find any package that can help me out. Any suggestions?

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