R: Calculate differential expression between conditions using...
calculateTtest
R Documentation
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.
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
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(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
>