Description Usage Arguments Value Author(s) References See Also Examples
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.
1 2 |
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.
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.
1 2 | rp <- data.frame(paste("g", 1:100), matrix(runif(500,0,1), 100, 5))
IsoBHPlot(rp, FDR = 0.05, stat = "E2")
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