replicateCorrelations {clippda} | R Documentation

## A generic function to compute intraclass correlations

### Description

This generic function computes intraclass correlations for duplicate peak data.

### Usage

    replicateCorrelations(Data, ...)

### Arguments

`Data` | An object of `aclinicalProteomicsData` class.
`...` | Some methods for this generic function may take additional, optional arguments. At present none do.

### Value

`consensus:` | consensus intraclass correlation.
`correlations:` | intraclass correlations for each peak.

### Author(s)

Stephen Nyangoma

### References

Nyangoma SO, Ferreira JA, Collins SI, Altman DG, Johnson PJ, and Billingham LJ: Sample size calculations for planning clinical proteomic profiling studies using mass spectrometry. Bioinformatics (Submitted)

Smyth GK, et al.: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21, 2067 - 75

Smyth GK: Linear models and emperical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3, 1, Article 3

### Examples

    data(liverdata)

    data(liver_pheno)

    OBJECT=new("aclinicalProteomicsData")

    OBJECT@rawSELDIdata=as.matrix(liverdata)
    OBJECT@covariates=c("tumor" ,    "sex")
    OBJECT@phenotypicData=as.matrix(liver_pheno)
    OBJECT@variableClass=c('numeric','factor','factor')
    OBJECT@no.peaks=53

    replicateCorrelations(OBJECT)

[Package clippda version 1.40.0 Index]