I currently have a program that automates 2-way ANOVA on a series of endpoints,
but before the ANOVA is carried out I want the code to test the assumptions of
normality and equal variance and report along with each anova result in the
output file. How can I do this?
I have pasted below the code that I currently use.
library(car)
numFiles = x # <--<--<--<--<--<--<--<--<--<--<-- supply the number of files
containing the source data here
for (iIndx in 1:numFiles) {
sinkFilePath = paste("C:/AnovaData/2WayAnovaForProteins_Set", iIndx,
".txt", sep="")
sink(sinkFilePath)
sourceFilePath = paste("C:/AnovaData/ProteinsFor2WayAnova_Set", iIndx, ".txt",
sep="")
dataSet = read.delim(sourceFilePath)
numProteins = ncol(dataSet)
nameProteins = colnames(dataSet)
for (i in 3:numProteins) {
fla = as.formula(paste(nameProteins[i],"~","Trt*Dose"))
mod = lm(fla, data = dataSet , contrasts = list(Trt = contr.sum, Dose =
contr.sum))
ano = Anova(mod, type = "III")
print.noquote("")
print.noquote("")
print.noquote("--------------------------------------------")
print.noquote(paste("--------- Analysis of Spot:
",nameProteins[i],"------------"))
print.noquote("--------------------------------------------")
print(ano)
}
}
Thanks in advance.
Karthi
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