doPlotEset: Produce a number of QA plot plus t and ANOVA test
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
Value
None. A number of plots and t or ANOVA test result file will be
produced.
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.
#-doPlotEset(eset, "sampleGroup")#-doPlotEset(eset, "sampleGroup", name = "perfect")#-doPlotEset(eset, "sampleGroup", test = FALSE) ##- t test will be not performed