LMGene
(Package: LMGene) :
LMGene main function
LMGene calls function genediff to calculate the unadjusted gene-specific and posterior p-values of all genes and then calculates the FDR-adjusted p-values of all genes. Significant genes for each factor in model (based on either the gene-specific or posterior FDR-adjusted p-values) are output.
● Data Source:
BioConductor
● Keywords:
● Alias: LMGene
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Computes two sets of p-values per gene or probe via gene-by-gene ANOVA, using both the gene-specific MSE and the posterior MSE for each term in the ANOVA. P-values are not adjusted for multiple testing.
Assumes a fixed effects model and that the correct denominator for all comparisons is the MSE.
● Data Source:
BioConductor
● Keywords: models
● Alias: genediff
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glog
(Package: LMGene) :
Generalized log transformation function
This function transforms the input values by the generalized log function.
● Data Source:
BioConductor
● Keywords: math
● Alias: glog
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lnorm
(Package: LMGene) :
Lowess normalization function
Lowess normalization function
● Data Source:
BioConductor
● Keywords: smooth
● Alias: lnorm
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lnormeS
(Package: LMGene) :
Function to apply lowess normalization to an expression set.
Like lnorm, but applies to and returns an ExpressionSet or AffyBatch object instead of a matrix.
● Data Source:
BioConductor
● Keywords: smooth
● Alias: lnormeS
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neweS
(Package: LMGene) :
Coerce a matrix to class ExpressionSet
This function converts a data matrix into an ExpressionSet object.
● Data Source:
BioConductor
● Keywords: manip
● Alias: neweS
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norm
(Package: LMGene) :
Normalization function
This function normalizes a matrix by subtracting the column (sample) mean from each element and adding the grand mean.
● Data Source:
BioConductor
● Keywords:
● Alias: norm
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Plots the row standard deviation of a matrix of expression data against the row mean, or the rank of the row mean.
● Data Source:
BioConductor
● Keywords: dplot
● Alias: plotMeanSD
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psmeans
(Package: LMGene) :
Function to take means of probesets.
Converts an ExpressionSet or AffyBatch object with one row of expression data per probeset into an ExpressionSet or AffyBatch object with one row per probe.
● Data Source:
BioConductor
● Keywords: manip
● Alias: psmeans
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pvadjust
(Package: LMGene) :
P-value adjusting function
This function converts the given raw p-values into the FDR adjusted p-values using R package 'multtest'.
● Data Source:
BioConductor
● Keywords: models
● Alias: pvadjust
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providing 
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