LMGene {LMGene} | R Documentation |
LMGene calls function genediff
to calculate the raw p-values of all genes
and then calls function pvadjust
to calculate the adjusted p-values of all genes.
Finally, calls function rowlist
to list the names of genes that are selected as significant under the specified significance level.
LMGene(eS, level = 0.05)
eS |
Array data. must be exprSet type and the log-transformation and the normalization of exprSet@exprs are recommended. |
level |
Significance level |
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.
level
indicates False Discovery Rate. e.g.) level 0.05 means 5
lmres |
A list which contains significant gene names for each considered factor |
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) siggeneslist<-LMGene(LoggedSmpd0, 0.01) siggeneslist$x3