Use t Test to Compare Two Groups

Description

Use a (modified) t test to compare two groups

Usage

tTest(object, groups, probe2gene = TRUE)

Arguments

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

Author(s)

Willem Talloen, Tobias Verbeke

See Also

rowttests

Examples

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)  
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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'help.start()' for an HTML browser interface to help.
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> library(a4Base)
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':

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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    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: AnnotationDbi
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Attaching package: 'S4Vectors'

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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
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Attaching package: 'MASS'

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

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Attaching package: 'gplots'

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a4Base version 1.20.0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/tTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tTest
> ### Title: Use t Test to Compare Two Groups
> ### Aliases: tTest
> ### Keywords: htest
> 
> ### ** Examples
> 
> 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)  
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


> 
> 
> 
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> 
> dev.off()
null device 
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