genediff {LMGene}R Documentation

Raw p-value calculation function

Description

Computes two vectors of p-values per gene or probe using gene-by-gene anova with individual gene MSE using both the gene-specific MSE and the posterior mean MSE for each term in the anova.
Assumes a fixed effects model and the correct denominator for all comparisons is the MSE

Usage

genediff(eS)

Arguments

eS Array data. must be a exprSet type and the log-transformation and the normalization of exprSet@exprs are recommended

Details

The input argument, eS, must be exprSet type from Biobase package. If you have a matrix data and information about the considered factors, then you can use neweS to conver the data into exprSet. Please see neweS in more detail.

Value

pvlist a list containing two sets of p-values obtained by gene specific MSE and the posterior MSE methods

Author(s)

David Rocke and Geun-Cheol Lee

References

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/

See Also

LMGene, rowaov

Examples

#library
library(Biobase)
library(LMGene)

#data
data(Smpd)
data(vlist)
LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist)

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


[Package LMGene version 1.0.0 Index]