The GST plot displays the relative direction (in two conditions) and statistics ranking for genes in a gene set.
● Data Source:
CranContrib
● Keywords:
● Alias: GSTplot
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A gene set analysis function for one-sided test (OLS) and two-sided test (multivariate analysis of variance). Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented. MAVTgsa computes the p-values and FDR (false discovery rate) q-values for all gene sets. The p-values for individual genes in a significant gene set are also listed. MAVTgsa generates a GST-plot of the empirical distribution function of the ranked test statistics of a given gene set.
● Data Source:
CranContrib
● Keywords: one-sided test, MANOVA test, multiple comparisons, OLS test, gene set analysis, GST-plot
● Alias: MAVTgsa, MAVTgsa-package
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A gene set analysis functions for computiong the p-values for one-sided test (OLS) and two-sided test (multivariate analysis of variance). If the experimental conditions are equal to 2, the p-value for Hotelling's t square test is calculated. If the experimental conditions are great than 2, the p-value for Wilks' Lambda is deterimined and post-hoc test is reported too. The p-value for individual gene test of significant gene sets are also listed.
● Data Source:
CranContrib
● Keywords: MANOVA test
● Alias: MAVTn
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To compute OLS statistic for one-sided test
● Data Source:
CranContrib
● Keywords: OLS
● Alias: Tols
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To compute Wilk's Lambda statistic for multivariate analysis of variance and multiple comparisons.
● Data Source:
CranContrib
● Keywords: Wilks' Lambda
● Alias: Wilksn
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MAVTp
(Package: MAVTgsa) :
Random Forests-based procedure
A Random Forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes.
● Data Source:
CranContrib
● Keywords: Random forests
● Alias: MAVTp
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a data matrix with 15 samples in column and one class type and 10 gene expression data in row.
● Data Source:
CranContrib
● Keywords:
● Alias: data
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Returns the p-values in each permutation.
● Data Source:
CranContrib
● Keywords:
● Alias: minp
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To construct a design matrix of the clinical outcome of the samples.
● Data Source:
CranContrib
● Keywords:
● Alias: design.matrix
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To compute Hotelling's T square statistic for multivariate analysis of variance using Shrinkage covariance matrix estimates.
● Data Source:
CranContrib
● Keywords:
● Alias: Hott2
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