puma (version 3.12.0)

pumaClustii: Propagate probe-level uncertainty in robust t mixture clustering on replicated gene expression data

Description

This function clusters gene expression by including uncertainties of gene expression measurements from probe-level analysis models and replicate information into a robust t mixture clustering model. The inputs are gene expression levels and the probe-level standard deviation associated with expression measurement for each gene on each chip. The outputs is the clustering results.

Usage

pumaClustii(e=NULL, se=NULL, efile=NULL, sefile=NULL,  subset=NULL, gsnorm=FALSE, mincls, maxcls, conds, reps, verbose=FALSE, eps=1.0e-5, del0=0.01)

Arguments

e

data frame containing the expression level for each gene on each chip.

se

data frame containing the standard deviation of gene expression levels.

efile

character, the name of the file which contains gene expression measurements.

sefile

character, the name of the file which contains the standard deviation of gene expression measurements.

subset

vector specifying the row number of genes which are clustered on.

gsnorm

logical specifying whether do global scaling normalisation or not.

mincls

integer, the minimum number of clusters.

maxcls

integer, the maximum number of clusters.

conds

integer, the number of conditions.

reps

vector, specifying which condition each column of the input data matrix belongs to.

verbose

logical value. If 'TRUE' messages about the progress of the function is printed.

eps

numeric, optimisation parameter.

del0

numeric, optimisation parameter.

Value

The result is a list with componentscluster: vector, containing the membership of clusters for each gene; centers: matrix, the center of each cluster; centersigs: matrix, the center variance of each cluster; likelipergene: matrix, the likelihood of belonging to each cluster for each gene; optK: numeric, the optimal number of clusters. optF: numeric, the maximised value of target function.

Details

The input data is specified either by e and se, or by efile and sefile.

References

Liu,X. and Rattray,M. (2009) Including probe-level measurement error in robust mixture clustering of replicated microarray gene expression, Statistical Application in Genetics and Molecular Biology, 9(1), Article 42.

Liu,X., Lin,K.K., Andersen,B., and Rattray,M. (2007) Propagating probe-level uncertainty in model-based gene expression clustering, BMC Bioinformatics, 8:98.

Liu,X., Milo,M., Lawrence,N.D. and Rattray,M. (2005) A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips, Bioinformatics, 21(18):3637-3644.

See Also

Related method mmgmos and pumaclust

Examples

  data(Clustii.exampleE)
  data(Clustii.exampleStd)
  r<-vector(mode="integer",0)
  for (i in c(1:20))
    for (j in c(1:4))
      r<-c(r,i)
  cl<-pumaClustii(Clustii.exampleE,Clustii.exampleStd,mincls=6,maxcls=6,conds=20,reps=r,eps=1e-3)