doANOVA: Perform one way or two way ANOVA

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

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.

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.

Value

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

Author(s)

Y Andrew Sun

Examples

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

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

Example output

Welcome to Applied Biosystems AB1700
    This package performs analysis for AB1700
    gene expression data

Warning message:
no DISPLAY variable so Tk is not available 

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