rowlist {LMGene} | R Documentation |
This function makes significant gene list for a specified factor, where genes are selected as significant by the given p-values and significance level.
rowlist(genemat, effnum, apvlist, level, posterior = TRUE)
genemat |
A matrix data of array |
effnum |
Factor number |
apvlist |
A vector with FDR adjusted p-value |
level |
Significance level |
posterior |
TRUE, if adjusted p-values are to be computed with Posterior method. |
genemat
is an n-by-p matrix of expression values
effnum
is the coumn number for the effect of interest
apvlist
is a matrix of p-values from pvadjust or genediff
the routine returns a list of genes whose FDR p-value is
less than level using either individual gene or posterior
MSE's. This function returs gene names if rownames(genemat) is not null,
or gene numbers otherwise.
level
indicates False Discovery Rate. e.g.) level 0.05 means 5
genelist |
A vector containing gene names if rownames(genemat) is not null, or gene numbers otherwise |
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(sample.mat) data(vlist) LoggedSmpd0<-neweS(lnorm(log(sample.mat)),vlist) pvlist<-genediff(LoggedSmpd0) apvlist<-pvadjust(pvlist) genelist<-rowlist(LoggedSmpd0@exprs,2,apvlist,0.01) genelist