| 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 column 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 returns 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(exprs(LoggedSmpd0), 2, apvlist, 0.01) genelist