IsoBHPlot {IsoGene} | R Documentation |
The function produces a plot with adjusted p-values using BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutilie 2004) procedures controlling for FDR. The raw p-values and adjusted BH and BY p-values are plotted.
IsoBHPlot(rp, FDR, stat = c("E2", "Williams", "Marcus", "M", "ModifM"))
rp |
raw p-value matrix with each row for one gene and 6 columns, the first column contains the Probe.ID, the second to the sixth columns are raw p-values for the five test statistics |
FDR |
the desired FDR to control |
stat |
choose one of the five test statistic to use |
A plot of adjusted p-values using BH and BY procedures will be produced.
Lin et al.
Testing for Trend in Dose-Response Microarray Experiments: a Comparison of Testing Procedures, Multiplicity, and Resampling-Based Inference, Lin et al. 2007, Stat. App. in Gen. & Mol. Bio., 6(1), article 26.
rp <- data.frame(paste("g", 1:100), matrix(runif(500,0,1), 100, 5)) IsoBHPlot(rp, FDR = 0.05, stat = "E2")