Only after doing the best I could with univariate modeling would I then consider multivariate modeling. And then I'd want to think very carefully about whether the multivariate model(s) under consideration seemed consistent with the univariate results -- and what else they might tell me that I hadn't already gotten from the univariate model. If you've already done all this, I'm impressed. In the almost 30 years since I realized I should try univariate models first and work up to multivariate whenever appropriate, I've not found one application where the extra effort seemed justified. R has made this much easier, but I'm still looking for that special application that would actually require the multivariate tools.
To add to Spencer's comments, I'd strongly recommend you look at your data before trying to model it. The attached graph, a scatterplot of res1 vs res2 values conditional on c1 and c2, with point shape given by inter, reveals many interesting features of your data: * res1 and res2 values are highly correlated * inter is constant for a given c1 and c2 * there are between 1 and 3 points for each level of inter - not very many and I don't think enough to investigate what the effect of inter is The plot was created using the following code: library(ggplot) s <- read.table("~/Desktop/sample.txt", header=T) s <- rename(s, c(two="value")) s$res2 <- NULL s <- as.data.frame(cast(s, ... ~ res1)) qplot(X0, X1, c1 ~ c2, data=s, shape=factor(inter)) (note that you will need the latest version of ggplot available from http://had.co.nz/ggplot)
graph.pdf
Description: Adobe PDF document
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