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


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Documentation for package ‘LMGene’ version 2.26.0

Help 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 probe-level Affymetrix expression data
transeS Function to apply the glog transform to an expression set.
vlist Sample experimental/phenotype data for LMGene package