If only one factor is provided in parameter, one way ANOVA is performed. If two factors are provided, two way ANOVA is performed.
1  doANOVA(eset, group1, group2, snThresh = 3, detectSample = 0.5)

eset 
An 
group1 
A factor name or labels to test on. If eset is an

group2 
A factor name or labels to test on. 
snThresh 
Using probes detectable for ANOVA analysis, default S/N value is 3 or more to be considered detectable. 
detectSample 
The percentage of samples the probe is detected in order to be considered in ANOVA analysis. 
At least one group should be provided. If ExpressionSet
object
is used, group1 or group2 is the name of the sampleGroup defined in
experiment design file. If labels are to be used, they can be either
numeric or text, e.g., c(1,1,2,2,3,3) or c("treat1", "treat1", "treat2",
"treat2", "treat3", "treat3").
If the probe is detectable in 50% (default) or more samples in any one of the subgroup, it is included in the ANOVA analysis.
a vector if one way ANOVA; a matrix if two way ANOVA
Y Andrew Sun
1 2 3 4 5  # one way ANOVA
# anova < doANOVA(eset, "sampleGroup")
# two way ANOVA
# anova < doANOVA(eset, "sampleGroup1", "sampleGoup2")

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