test {applera} | R Documentation |
This dataset is used to test the functionalities of the applera package
data(test)
An appleraSet object
Raffaele A. Calogero lab. <raffaele.calogero@unito.it>
data(test) #brief description of the appleraSet test #available slots slotNames(test) #accessing to the Organism organism(test) #accessing to the Geneid #geneid(test) #accessing to the Signal values # exprs(signal(test)[1:2,]) #phenoData associated to the Signal slot # pData(signal(test)) #histograms of the slots of appleraSet # hist(test) #boxplot of the slots of appleraSet # boxplot(test) #mva.pairs plot of the wk15 # samples<-sampleNames(signal(test))[which(signal(test)$wk==15)] # mvaAp(subExp(test, samples)) #subsetting genes by geneNames # tmp<-geneNames(signal(test))[1:5] # tmp.1<-subGenes(test, tmp) #performing loess normalization for the appleraSet # test.norm<-normLoess(test) #Filtering by signal/noise, keep genes where at least 50 # sn.subset <- apFilter(test, 0.5, 3, "sn") #Filtering by signal/noise, keep genes where at least 50 # flags.subset <- apFilter(test, 0.5, 2, "flags") #Filtering by IQR, # iqr.sn.subset<-iqrFilter(sn.subset, 0.25)