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, model=NULL)

Arguments

eS Array data. must be an ExpressionSet object and the log-transformation and the normalization of exprs(eS) are recommended.
model Model used for comparison; see details and LMGene.

Details

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

The model argument is an optional character string, constructed like the right-hand side of a formula for lm. It specifies which of the variables in the ExpressionSet will be used in the model and whether interaction terms will be included. If model=NULL, it uses all variables from the ExpressionSet without interactions. Be careful of using interaction terms with factors; this often leads to overfitting, which will yield an error.

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

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

[Package LMGene version 1.12.0 Index]