doPlotEset {ABarray} | R Documentation |
Produce boxplot, MA plot, scatter plot, correlation, S/N detection concordance, CV, and t test, ANOVA test if subgroup is more than 2
doPlotEset(eset, group, name = "", snThresh = 3, test = TRUE, ...)
eset |
eset eset an exprSet 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 |
We use se.exprs
slot of exprSet
to store S/N ratio
data. This is currently implemented in ABarray
function. The
exprSet
returned from ABarray
will have S/N ratio in the
se.exprs
slot. If se.exprs
contains S/N ratio, then
various calculations will be filtered using parameter snThresh
(default = 3). To change snThresh, supply new threshold in the
parameter.
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.
None. A number of plots and t or ANOVA test result file will be produced.
Y Andrew Sun
#-doPlotEset(eset, "sampleGroup") #-doPlotEset(eset, "sampleGroup", name = "perfect") #-doPlotEset(eset, "sampleGroup", test = FALSE) ##- t test will be not performed