Hello, I'm trying to reproduce some SAS result wit R (after I got suspicious with the result in R). I struggle with the contrasts in a linear model.
I've got three factors > d$dose <- as.factor(d$dose) # 5 levels > d$time <- as.factor(d$time) # 2 levels > d$batch <- as.factor(d$batch) # 3 levels the data frame d contains 82 rows. There are 2 to 4 replicates of each dose within each time point and each batch. There's one dose completely missing from one batch. I then generate Dunnett contrasts using the multicomp library: > contrasts(d$dose) <- contr.Dunnett(levels(d$dose), 1) > contrasts(d$time) <- contr.Dunnett(levels(d$time), 1) > contrasts(d$batch) <- contr.Dunnett(levels(d$batch), 1) For the moment I'm just looking at the dose effects of the complete model: > summary(lm(value ~ dose * time * batch, data = d))$coefficients[1:5,] Estimate Std. Error t value Pr(>|t|) (Intercept) 6.80211741 0.01505426 451.8399839 1.962247e-101 dose010mM-000mM -0.03454211 0.04113846 -0.8396549 4.046723e-01 dose025mM-000mM -0.01972550 0.04288981 -0.4599111 6.473607e-01 dose050mM-000mM -0.12015983 0.05356935 -2.2430704 2.886726e-02 <- significant dose100mM-000mM 0.01252061 0.04113846 0.3043529 7.619872e-01 A collegue of mine has run the same data through a SAS program (listed below) proc glm data = dftest; class dose time batch; model value = dose|time|batch; means dose / dunnett ('000mM'); lsmeans dose /pdiff singular=1; run; Giving the following p-values: Pr(>|t|) dose010mM-000mM 0.4047 dose025mM-000mM 0.6474 dose050mM-000mM 0.5745 <--- dose100mM-000mM 0.7620 The p-values are the same expect for the one indicated. A stripchart for the data in R shows that "dose050mM-000mM" should not be significant (it doesn't look different from e.g. "dose025mM-000mM"). Do you've any suggestions what I'm doing wrong here (assuming that I believe the SAS result)? Any hints what I can do to further analyse this problem? Many thanks for your help, +regards, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html