doPlotEset: Produce a number of QA plot plus t and ANOVA test

In ABarray: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

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

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

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

ABarray documentation built on Nov. 8, 2020, 5:25 p.m.