Tools for Meta-analysis of gene expression data.

Description

A small number of meta-analysis functions for comparing two gene expression experiments are provided.

Usage

dstar(d, n)
getdF(data, categ)
sigmad(d, ng1, ng2)

Arguments

Details

The functions getdF compute t-test statistics for the input data and group membership (note that group membership must be indicated by a vector of 0's and 1's).

The function dstar computes an unbiased estimate of the t-test. The function sigmad computes the variance estimate of dstar.

Value

The different functions have different return values, but generally they are vectors of the requested quantities.

Author(s)

L. Lusa, R. Gray and R. Gentleman

References

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 2003, i84-i90.

Examples

  x = matrix(rnorm(1000), ncol=10)
  ds = getdF(x, rep(c(0,1), c(5,5)))
  dst = dstar(ds, ncol(x))
  sgd = sigmad(ds, 5, 5)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GeneMeta)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GeneMeta/dstar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dstar
> ### Title: Tools for Meta-analysis of gene expression data.
> ### Aliases: dstar sigmad getdF getdF,ExpressionSet,numeric-method
> ###   getdF,matrix,numeric-method
> ### Keywords: htest
> 
> ### ** Examples
> 
>   x = matrix(rnorm(1000), ncol=10)
>   ds = getdF(x, rep(c(0,1), c(5,5)))
>   dst = dstar(ds, ncol(x))
>   sgd = sigmad(ds, 5, 5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>