clippda (version 1.22.0)

sampleSizeParameters: A generic function to calculate sample size parameters

Description

This generic function computes input parameters for the sample size calculation function.

Usage

sampleSizeParameters(Data,intraclasscorr,signifcut, ...)

Arguments

Data

An object of aclinicalProteomicsData class.

intraclasscorr

An object of numeric class. It is a known value of the intraclass correlation, or an estimate from a pilot data.

signifcut

An object of numeric class. It is significance threshold (usually, taken to be 0.05 in the analysis of the protein profiling studies).

...

Some methods for this generic function may take additional, optional arguments. At present none do.

Value

Corr

the intraclass correlation from your pilot data.

techVar

the technical variance from your pilot data.

bioVar

the biological variance from your pilot data.

DIFF

the clinically important difference from your pilot data.

no.peaks

the number of peaks detected by the Biomarker wizard.

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, 2009, 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

intraclasscorr  <-  0.60 #cut-off for intraclass correlation

signifcut <- 0.05      #significance cut-off

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


sampleSizeParameters(OBJECT,intraclasscorr,signifcut)