tTest: Use t Test to Compare Two Groups

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/tTest.R

Description

Use a (modified) t test to compare two groups

Usage

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tTest(object, groups, probe2gene = TRUE)

Arguments

object

ExpressionSet object

groups

string indicating the name of the variable of the phenoData containing the group information

probe2gene

logical; if TRUE Affymetrix probeset IDs are translated into gene symbols; if FALSE no such translation is conducted

Details

For multiple testing the mt.rawp2adjp function of package multtest is used.

Value

Object of class "tTest", a data frame with the following columns

gSymbol

Gene Symbol

p

TODO

logRatio

TODO

pBH

TODO

tStat

TODO

Author(s)

Willem Talloen, Tobias Verbeke

See Also

rowttests

Examples

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if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))

  tTestRes <- tTest(object = ALL,	groups = "BTtype", probe2gene = TRUE)
  volcanoPlot(tTestRes)  
}

Example output

Loading required package: grid
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: annaffy
Loading required package: GO.db

Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: mpm
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-22

Loading required package: genefilter

Attaching package: 'genefilter'

The following object is masked from 'package:MASS':

    area

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: multtest
Loading required package: glmnet
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: a4Preproc
Loading required package: a4Core

Attaching package: 'a4Core'

The following object is masked from 'package:limma':

    topTable

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:multtest':

    wapply

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess


a4Base version 1.24.0

Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db

a4Base documentation built on April 29, 2020, 5:17 a.m.

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