export.res {varmixt} | R Documentation |
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.
export.res(data,filename=NULL,header=TRUE,comment=NULL,lambda=seq(0,0.95,0.05))
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 |
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 |
Paul Delmar
vm.analysis
, vm.analysis.paired