PairContrast
(Package: maanova) :
Pairwise comparison matrix
It returns all possible pairwise comparison.
● Data Source:
BioConductor
● Keywords: models
● Alias: PairContrast
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Rmaanova.version
(Package: maanova) :
Display the current version of the package
This is the function to display the current verion number of R/maanova pakcage.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: Rmaanova.version
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adjPval
(Package: maanova) :
Generate FDR adjusted P values for F test result.
This function takes a result object from matest and calculate the FDR adjusted P values. The new P values will be appended to the input object as additional fields. It has four options; "stepup" (Hochberg and Benjamini, 1990), "adaptive" (Benjamini and Hochberg, 2000), "stepdown" (Westfall and Young, 1993) and "jsFDR" (Storey, 2002). "jsFDR" option uses 'qvalue' package by John Storey and user suppose to install 'qvalue' package before using this option. There is no default option, thus you need to specify one option.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: adjPval
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arrayview
(Package: maanova) :
View the layout of input data
This function reconstructs the input data according to the Microarray grid location structure and plots the data according to the user specified color map.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: arrayview
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consensus
(Package: maanova) :
Build consensus tree out of bootstrap cluster result
This is the function to build the consensus tree from the bootstrap clustering analysis. If the clustering algorithm is hierarchical clustering, the majority rule consensus tree will be built based on the given significance level. If the clustering algorithm is K-means, a consensus K-means group will be built.
● Data Source:
BioConductor
● Keywords: cluster
● Alias: consensus
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dyeswapfilter
(Package: maanova) :
Gene filter for dye-swap experiment
This function is used to flag the questionable spot in any kind of dye-swap experiment.
● Data Source:
BioConductor
● Keywords: models
● Alias: dyeswapfilter
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This is the function to do missing data imputation.
● Data Source:
BioConductor
● Keywords: utilities
● Alias: fill.missing
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fitmaanova
(Package: maanova) :
Fit ANOVA model for Micro Array experiment
This is the function to fit the ANOVA model for Microarray experiment. Given the data and formula, this function fits the regression model for each gene and calculates the ANOVA estimates, variance components for random terms, fitted values, etc. For a mixed effect models, the output estimates will be BLUE and BLUP.
● Data Source:
BioConductor
● Keywords: models
● Alias: fitmaanova
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fom
(Package: maanova) :
Figure of Merit
K-means clustering needs a given number of groups, which is difficult to guess in most of the cases. This function calculates the Figure of Merit values for different number of groups and generates the FOM plot (FOM value versus number of groups). Lower FOM value means better grouping. User can decide the number of groups in kmeans cluster based on that result.
● Data Source:
BioConductor
● Keywords: models
● Alias: fom
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geneprofile
(Package: maanova) :
Expression plot for selected genes
This function generate a plot with many lines. Each line represents a gene. The y-axis is the estimated expression level for the given factor from ANOVA model. The x-axis is for the levels of the give factor, e.g., different strains.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: geneprofile
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