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| * R Code to Perform the Benjamini and Hochberg FDR procedure [Insert P values in any order] | === R Code to Perform the Benjamini and Hochberg FDR procedure === |
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| ''' pvalue <- c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) sorted.pvalue<-sort(pvalue) sorted.pvalue j.alpha <- (1:10)*(.05/10) diff <- sorted.pvalue-j.alpha neg.diff <- diff[diff<0] pos.diff <- neg.diff[length(neg.diff)] index <- diff==pos.diff p.cutoff <-sorted.pvalue[index] p.cutoff p.sig <- pvalue[pvalue <= p.cutoff] p.sig |
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| R Output > pvalue<-c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) > sorted.pvalue <- sort(pvalue) > sorted.pvalue | [Insert P values in any order] pvalue <- c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) sorted.pvalue<-sort(pvalue) sorted.pvalue j.alpha <- (1:10)*(.05/10) diff <- sorted.pvalue-j.alpha neg.diff <- diff[diff<0] pos.diff <- neg.diff[length(neg.diff)] index <- diff==pos.diff p.cutoff <-sorted.pvalue[index] p.cutoff p.sig <- pvalue[pvalue <= p.cutoff] p.sig }}} === R Output === {{{ > pvalue<-c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) > sorted.pvalue <- sort(pvalue) > sorted.pvalue |
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| [1] 0.001 0.005 0.017 0.021 0.023 0.036 0.041 0.042 0.070 0.100 | |
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| [1] 0.001 0.005 0.017 0.021 0.023 0.036 0.041 0.042 0.070 0.100 > j.alpha <- (1:10) * (0.05/10) > diff <- sorted.pvalue - j.alpha > neg.diff <- diff[diff < 0] > pos.diff <- neg.diff[length(neg.diff)] > index <- diff == pos.diff > p.cutoff <- sorted.pvalue[index] > p.cutoff [1] 0.023 > p.sig <- pvalue[pvalue <= p.cutoff] > p.sig | > j.alpha <- (1:10) * (0.05/10) > diff <- sorted.pvalue - j.alpha > neg.diff <- diff[diff < 0] > pos.diff <- neg.diff[length(neg.diff)] > index <- diff == pos.diff > p.cutoff <- sorted.pvalue[index] > p.cutoff [1] 0.023 |
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| [significant p values by B-H method]: [1] 0.021 0.001 0.017 0.005 0.023 ''' |
> p.sig <- pvalue[pvalue <= p.cutoff] > p.sig [significant p values by B-H method]: [1] 0.021 0.001 0.017 0.005 0.023 }}} |
R Code to Perform the Benjamini and Hochberg FDR procedure
[Insert P values in any order] pvalue <- c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) sorted.pvalue<-sort(pvalue) sorted.pvalue j.alpha <- (1:10)*(.05/10) diff <- sorted.pvalue-j.alpha neg.diff <- diff[diff<0] pos.diff <- neg.diff[length(neg.diff)] index <- diff==pos.diff p.cutoff <-sorted.pvalue[index] p.cutoff p.sig <- pvalue[pvalue <= p.cutoff] p.sig
R Output
> pvalue<-c(0.021,0.001,0.017,0.041,0.005,0.036,0.042,0.023,0.07,0.1) > sorted.pvalue <- sort(pvalue) > sorted.pvalue [sorted P values in ascending order] [1] 0.001 0.005 0.017 0.021 0.023 0.036 0.041 0.042 0.070 0.100 > j.alpha <- (1:10) * (0.05/10) > diff <- sorted.pvalue - j.alpha > neg.diff <- diff[diff < 0] > pos.diff <- neg.diff[length(neg.diff)] > index <- diff == pos.diff > p.cutoff <- sorted.pvalue[index] > p.cutoff [1] 0.023 > p.sig <- pvalue[pvalue <= p.cutoff] > p.sig [significant p values by B-H method]: [1] 0.021 0.001 0.017 0.005 0.023