Nothing
IsoBHPlot <- function(rp, FDR, stat = c("E2", "Williams", "Marcus", "M", "ModifM")){
stat <- match.arg(stat)
Probe.ID <- rp[, 1]
rpraw <- switch(stat,
E2 = rp[, 2],
Williams = rp[, 3],
Marcus = rp[, 4],
M = rp[, 5],
ModifM = rp[, 6])
#procs <- c("Bonferroni", "Holm", "BH", "BY")
#res <- mt.rawp2adjp(rpraw, procs) # from multtest
#adjp <- res$adjp[order(res$index), ]
adjp <- cbind(rpraw, p.adjust(rpraw, "BH"),p.adjust(rpraw,"BY"))
plot(1:nrow(rp), sort(adjp[,1]),
col = 4, pch = ".", lty = 1, xlab = "index",
ylab = "Adjusted P values")
lines(1:nrow(rp), sort(adjp[,1]), lty = 1, col = 1)
lines(1:nrow(rp), sort(adjp[,2]), lty = 4, col = 2)
lines(1:nrow(rp), sort(adjp[,3]), lty = 5, col = 3)
abline(FDR, 0, lty = 6)
legend(nrow(rp) / 2,
0.3, col = c(1,2,3), c("Raw P","BH(FDR)","BY(FDR)"), lty = c(1,4:5))
title(paste(stat, ": Adjusted p values by BH and BY", sep = ""))
}
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