deGenesANOVA: Function to do differential expression analysis, using ANOVA...

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This function takes an object of class maiges and do differential expression analysis for the genes onto dataset, comparing more than two samples using ANalysis Of VAriance (ANOVA) models.

Usage

deGenesANOVA(data=NULL, eBayes=FALSE, retOrig=FALSE,
             retF=FALSE, doClust=TRUE, ...)

Arguments

data	object of class maigesANOVA.
eBayes	logical indicating the use or not (default) of empirical Bayes statistics implemented in limma package.
retOrig	logical indicating if the object of class MArrayLM from limma package must be returned. Defaults to FALSE.
retF	logical asking to return the results associated with the F test (TRUE) or with the individual contrasts (FALSE - default).
doClust	logical indicating if the object generated from this analysis will be used for cluster analysis. Defaults to TRUE.
...	additional parameters to function lmFit.

Details

The object of class maigesANOVA of the argument data is created by the function designANOVA. This function calculate statistics and p-values using the function lmFit from package limma.

Value

The result of this function is an object of class MArrayLM when retOrig is TRUE. When it is FALSE, the result is an object of class maigesDE if doClust if FALSE or of class maigesDEcluster if it is TRUE.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

designANOVA, lmFit, MArrayLM.

Examples

## Loading the dataset
data(gastro)

## Constructing a maigesANOVA object for the 'Tissue' sample label using
## default model (simple linear model with intercept) and contrasts (all
## parameters are equal between themselves)
gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")

## Fitting the ANOVA model designed by the above command
gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)
gastro.ANOVAfit

Example output

Loading required package: convert
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: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: marray
Loading required package: graph
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied

Object of class maigesDEcluster generated by Fri Sep 25 12:29:33 2020, 
 using R version 3.4.4 (2018-03-15).

Classifying 487 genes as Differentialy Expressed (DE) 
 i  1 test(s).

The method used was ANOVA - F test.

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.