Produce a number of QA plot plus t and ANOVA test

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Description

Produce boxplot, MA plot, scatter plot, correlation, S/N detection concordance, CV, and t test, ANOVA test if subgroup is more than 2

Usage

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doPlotEset(eset, group, name = "", snThresh = 3, test = TRUE, ...)

Arguments

eset

an ExpressionSet object

group

name of the group from experiment design file

name

a name for use in output files for record purpose

snThresh

threshold of S/N considered detectable, default = 3

test

whether t or ANOVA test should be performed

...

Additional arguments, currently not implemented

Details

The t test and fold change is performed with function fctPlot. See additional information with fctPlot. ANOVA is performed with doANOVA.

If there are more than 2 subgroup in group, t test and fold change will be performed for each pair of subgroup and one way ANOVA will be performed. If subgroup is 2, ANOVA will not be performed.

Value

None. A number of plots and t or ANOVA test result file will be produced.

Author(s)

Y Andrew Sun

Examples

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#-doPlotEset(eset, "sampleGroup")
#-doPlotEset(eset, "sampleGroup", name = "perfect")
#-doPlotEset(eset, "sampleGroup", test = FALSE)  ##- t test will be not performed