replicateCorrelations: A generic function to compute intraclass correlations
In clippda: A package for the clinical proteomic profiling data analysis

Description Usage Arguments Value Author(s) References Examples

This generic function computes intraclass correlations for duplicate peak data.

1	replicateCorrelations(Data, ...)

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

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

Stephen Nyangoma

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

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)