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