normality and equal variance testing

Mon, Jan 24, 2011 1:02 PM

Why do you want to test for normality and equal variances?

If those are really a concern then you should use a method up front that is robust against those.  Those tests are usually testing a hypothesis that is different from what you are actually interested in and generally have low power to guide further tests.

Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111


> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
> project.org] On Behalf Of Karthi Subramanian
> Sent: Monday, January 24, 2011 10:06 AM
> To: R-devel at r-project.org
> Subject: [Rd] normality and equal variance testing
> 
> 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
> 
> 
> 	[[alternative HTML version deleted]]

normality and equal variance testing

Thread (3 messages)