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


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Documentation for package ‘LMGene’ version 1.16.0

User Guides and Package Vignettes

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genediff Raw p-value calculation function
GetLMObj Function to get a simple lm object for a regression on the relevant model.
glog Generalized log transformation function
jggrad2 Generating Jacobian-corrected data
jglog Glog
LMGene LMGene main function
lnorm Lowess normalization function
lnormeS Function to apply lowessnorm to a transformed expression set. Returns the normalized expression set.
mlm2lm Linear Model converting function
msa Relative mean square calculation function
msecalc MSE calculation function
msecalcmult MSE calculation function
neweS Coercing to an ExpressionSet code
norm Additive normalization function
psmeans Function to take means of probesets.
pvadjust P-value adjusting function
rowaov Gene by gene ANOVA function
rowlist Gene name listing 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
tranest2 Glog transformation parameter estimation function 2
tranestmult Glog transformation parameter estimation function for multiple parameters
transeS Function to apply the glog transform to an expression set. Returns the transformed expression set (not normalized).
vlist Sample experimental data for LMGene package