Calculate differential expression between conditions using T-test

Description

Automatically creates design and contrast matrices if not specified. This function is useful for comparing T-test results with those of other differential expression (DE) methods such as pumaDE.

Usage

calculateTtest(
	eset
,	design.matrix = createDesignMatrix(eset)
,	contrast.matrix = createContrastMatrix(eset)
)

Arguments

Details

The eset argument must be supplied, and must be a valid ExpressionSet object. Design and contrast matrices can be supplied, but if not, default matrices will be used. These should usually be sufficient for most analyses.

Value

An object of class DEResult.

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, calculateLimma, calculateFC, createDesignMatrix and createContrastMatrix and class DEResult

Examples

	eset_test <- new("ExpressionSet", exprs=matrix(rnorm(400,8,2),100,4))
	pData(eset_test) <- data.frame("class"=c("A", "A", "B", "B"))
	TtestRes <- calculateTtest(eset_test)
	plotErrorBars(eset_test, topGenes(TtestRes))

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)

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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.
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> library(puma)
Loading required package: oligo
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

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/puma/calculateTtest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateTtest
> ### Title: Calculate differential expression between conditions using
> ###   T-test
> ### Aliases: calculateTtest
> ### Keywords: manip
> 
> ### ** Examples
> 
> 	eset_test <- new("ExpressionSet", exprs=matrix(rnorm(400,8,2),100,4))
> 	pData(eset_test) <- data.frame("class"=c("A", "A", "B", "B"))
> 	TtestRes <- calculateTtest(eset_test)
> 	plotErrorBars(eset_test, topGenes(TtestRes))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>