clippda (version 1.22.0)

replicateCorrelations: 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.

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')
[e-mail]=53

replicateCorrelations(OBJECT)