deGenesANOVA {maigesPack} | R Documentation |
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.
deGenesANOVA(data=NULL, eBayes=FALSE, retOrig=FALSE, retF=FALSE, doClust=TRUE, ...)
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 . |
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.
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.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
## 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