IsoGene (version 1.0-24)

IsoBHPlot: Plot of adjusted p-values using BH or BY adjustment

Description

The function produces a plot with adjusted p-values using BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) procedures controlling for FDR. The raw p-values and adjusted BH and BY p-values are plotted.

Usage

IsoBHPlot(rp, FDR, stat = c("E2", "Williams", "Marcus",
"M", "ModifM"))

Arguments

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

Value

A plot of adjusted p-values using BH and BY procedures will be produced.

References

Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R, Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors), (2012), Springer.

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.

IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments, Pramana S., Lin D., Haldermans P., Shkedy Z., Verbeke T., De Bondt A., Talloen W., Goehlmann H., Bijnens L. 2010, R Journal 2/1.

See Also

IsoTestBH, IsoRawp

Examples

  rp <- data.frame(paste("g", 1:100), matrix(runif(500,0,1), 100, 5))
  IsoBHPlot(rp, FDR = 0.05, stat = "E2")