export.res {varmixt}R Documentation

Format and export analysis results

Description

This function builds a single data.frame with all the analysis results, computes the rank of genes based on their p-value and computes a ratio from the log-ratio.

Usage

export.res(data,filename=NULL,header=TRUE,comment=NULL,lambda=seq(0,0.95,0.05))

Arguments

data A gene expression data object. The results of vm.analysis of vm.analysis.paired function
filename the name of the output file. If NULL no file is written
header a logical value indicating whether the file contains the names of the variables as its first line.
comment
lambda

Value

a data.frame with all the analysis results, computes the rank of genes based on their p-value and computes a ratio from the log-ratio.

geneid gene name
ratio ratio
qual Number of low quality observations
pval.VM2 p-value with the variance mixture model
corrected.pval.VM2 corrected p-value with the variance mixture model(Bonferroni)
test.stat.VM2 test statistic with the variance mixture model
sigmadeltagVM2 standard deviation of deltag with the variance mixture model
group variance component (variance mixture model)
rank.p.VM2 rank according to the variance mixture model p-value
rank.p.VM rank according to the variance mixture model p-value without assigning gene to variance groups
rank.p.gene rank according to the gene-specific p-value
rank.p.anova rank according to the homoscedastic p-value
pval.gene p-value with the gene specific model
corrected.pval.gene corrected p-value with gene specific model (Bonferroni)
test.stat.gene test statistic with gene-specific model
sigmadeltag standard deviation of deltag with the gene-specific model
varg gene-specific variance of the gene
pval.anova p-value with the homoscedastic model
corrected.pval.anova corrected p-value with homoscedastic model (Bonferroni)
test.stat.anova test statistic with the homoscesatic model
sigmadeltaanova standard deviation of deltag with the homoscesatic model
pval.VM2 p-value with the variance mixture model without assigning genes to variance groups
corrected.pval.VM2 corrected p-value with the variance mixture model(Bonferroni) without assigning genes to variance groups
test.stat.VM test statistic with the continuous variance mixture model
sigmadeltagVM standard deviation of deltag with the continuous variance mixture model
rank.VM2 rank according to the variance mixture model test statistic
rank.gene rank according to homoscedastic test statistic
rank.anova rank according to homoscedastic test statistic
rank.VM rank according to the continuous variance mixture model test statistic
deltag mean log2-ratio
meanint mean log2-intensity

Author(s)

Paul Delmar

See Also

vm.analysis, vm.analysis.paired


[Package varmixt version 0.2-4 Index]