pvadjust: P-value adjusting function
In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

Description Usage Arguments Details Value Author(s) References See Also Examples

This function converts the given raw p-values into the FDR adjusted p-values using R package 'multtest'.

1	pvadjust(pvlist)

pvlist

A list containing raw p-values

pvlist is the output from genediff containing p-values from gene-specific MSE's and posterior MSE's.

pvlist2

A list with the raw p-values and the newly computed FDR adjusted p-values

David Rocke and Geun-Cheol Lee

David M. Rocke (2004), Design and analysis of experiments with high throughput biological assay data, Seminars in Cell & Developmental Biology, 15, 703-713.

http://www.idav.ucdavis.edu/~dmrocke/

genediff

#library
library(Biobase)
library(LMGene)

#data
data(sample.mat)
data(vlist)
LoggedSmpd0<-neweS(lnorm(log(sample.mat)),vlist)

pvlist<-genediff(LoggedSmpd0)
pvlist$Posterior[1:5,]

apvlist<-pvadjust(pvlist)
names(apvlist)
apvlist$Posterior.FDR[1:5,]