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

Share:

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

Author
David Rocke, Geun Cheol Lee, John Tillinghast, Blythe Durbin-Johnson, and Shiquan Wu
Date of publication
None
Maintainer
Blythe Durbin-Johnson <bpdurbin@ucdavis.edu>
License
LGPL
Version
2.30.0
URLs

View on Bioconductor

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

Files in this package

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