IsoTestBH: Test of monotonic trends using the five test statistics with BH or BY adjustment
Description
The function adjusts for the raw p-values of the five test statistics
using BH or BY procedure.
Usage
IsoTestBH(rp, FDR, type = c("BH", "BY"), 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
type
choose BH or BY procedure to control FDR
stat
choose one of the five test statistics to use
Value
sign.genes
A list of significant genes while controlling FDR is
obtained, with 4 columns: the first column is the probe ID, the
second column is the row id, the third column is the raw p-values of
the significant genes and the last column is the adjusted p-values
of significant genes using BH or BY procedure
Details
The input raw p-values to this function can be the one sided or the two
sided ones which are obtained using function raw.p. The results using
one sided p-values and FDR controlling at alpha/2 is equivalent to that
using two sided p-values and FDR controlling at alpha.
References
package multtest
Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens,
L. (editors). (2012) Modeling Dose-response Microarray
Data in Early Drug Development Experiments Using
R. Springer.
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.