genediff {LMGene} | R Documentation |
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
genediff(eS)
eS |
Array data. must be a exprSet type and the log-transformation and the normalization of exprSet@exprs are recommended |
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.
pvlist |
a list containing two sets of p-values obtained by gene specific MSE and the posterior MSE methods |
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/
#library library(Biobase) library(LMGene) #data data(Smpd) data(vlist) LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) pvlist<-genediff(LoggedSmpd0) pvlist$Posterior[1:5,]