ABarray (version 1.40.0)

doANOVA: Perform one way or two way ANOVA

Description

If only one factor is provided in parameter, one way ANOVA is performed. If two factors are provided, two way ANOVA is performed.

Usage

doANOVA(eset, group1, group2, snThresh = 3, detectSample = 0.5)

Arguments

eset

An ExpressionSet object.

group1

A factor name or labels to test on. If eset is an ExpressionSet object, either name or labels can be used. If eset is an expression matrix, labels should be used.

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.

Value

a vector if one way ANOVA; a matrix if two way ANOVA

Details

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.

Examples

  #- one way ANOVA
#-  anova <- doANOVA(eset, "sampleGroup")

  #- two way ANOVA
#-  anova <- doANOVA(eset, "sampleGroup1", "sampleGoup2")