LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
Version 2.32.0

LMGene package for analysis of microarray data using a linear model and glog data transformation

Browse man pages Browse package API and functions Browse package files

AuthorDavid Rocke, Geun Cheol Lee, John Tillinghast, Blythe Durbin-Johnson, and Shiquan Wu
Bioconductor views DifferentialExpression Microarray Preprocessing
Date of publicationNone
MaintainerBlythe Durbin-Johnson <bpdurbin@ucdavis.edu>
LicenseLGPL
Version2.32.0
URL http://dmrocke.ucdavis.edu/software.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LMGene")

Man pages

genediff: Gene-by-gene and posterior p-value calculation function.
glog: Generalized log transformation function
LMGene: LMGene main function
lnorm: Lowess normalization function
lnormeS: Function to apply lowess normalization to an expression set.
neweS: Coerce a matrix to class ExpressionSet
norm: Normalization function
plotMeanSD: Plotting function for gene means and standard deviations
psmeans: Function to take means of probesets.
pvadjust: P-value adjusting function
rowaov: Gene by gene ANOVA function
sample.eS: Sample array data for LMGene
sample.ind: Sample probeset index vector
sample.mat: Sample array data for LMGene package
tranest: Glog transformation parameter estimation function
tranestAffyProbeLevel: Glog transformation parameter estimation function for...
transeS: Function to apply the glog transform to an expression set.
vlist: Sample experimental/phenotype data for LMGene package

Functions

GetLMObj Source code
LMGene Man page Source code
arrayGlogSDStability Source code
fitFDist Source code
fitScaledF Source code
genediff Man page Source code
glog Man page Source code
jggrad2 Source code
jglog Source code
lnorm Man page Source code
lnormeS Man page Source code
mlm2lm Source code
msa Source code
msecalc Source code
msecalcmult Source code
neweS Man page Source code
norm Man page Source code
plotMeanSD Man page Source code
psmeans Man page Source code
pvadjust Man page Source code
rowaov Man page Source code
rowlist Source code
sample.eS Man page
sample.ind Man page
sample.mat Man page
tranest Man page Source code
tranest2 Source code
tranestAffyProbeLevel Man page Source code
tranestmult Source code
transeS Man page Source code
trigammaInverse Source code
vlist Man page

Files

DESCRIPTION
NAMESPACE
R
R/GetLMObj.R
R/LMGene.R
R/arrayGlogSDStability.R
R/fitFDist.R
R/fitScaledF.R
R/genediff.R
R/glog.R
R/jggrad2.R
R/jglog.R
R/lnorm.R
R/lnormeS.R
R/mlm2lm.R
R/msa.R
R/msecalc.R
R/msecalcmult.R
R/neweS.R
R/norm.R
R/plotMeanSD.R
R/psmeans.R
R/pvadjust.R
R/rowaov.R
R/rowlist.R
R/tranest.R
R/tranest2.R
R/tranestAffyProbeLevel.R
R/tranestmult.R
R/transeS.R
R/trigammaInverse.R
build
build/vignette.rds
data
data/sample.eS.RData
data/sample.ind.RData
data/sample.mat.RData
data/vlist.RData
inst
inst/doc
inst/doc/LMGene.R
inst/doc/LMGene.Rnw
inst/doc/LMGene.pdf
man
man/LMGene.Rd
man/genediff.Rd
man/glog.Rd
man/lnorm.Rd
man/lnormeS.Rd
man/neweS.Rd
man/norm.Rd
man/plotMeanSD.Rd
man/psmeans.Rd
man/pvadjust.Rd
man/rowaov.Rd
man/sample.eS.Rd
man/sample.ind.Rd
man/sample.mat.Rd
man/tranest.Rd
man/tranestAffyProbeLevel.Rd
man/transeS.Rd
man/vlist.Rd
vignettes
vignettes/LMGene.Rnw
LMGene documentation built on May 20, 2017, 9:19 p.m.