OK, now I am lost. I went from using aov(), which I fully understand, to lm() which I probably don't. I didn't specify a contrasts matrix in my call to lm().... Basically I want to find out if Infected/Uninfected affects the level of IL.4, and if Vaccinated/Unvaccinated affects the level of IL.4, obviously trying to separate the effects of Infection from the effects of Vaccination. The documentation for specifying contrasts to lm() is a little convoluted, sending me to the help file for model.matrix.default, and the help there doesn't really give me much to go on when trying to figure out what contrasts matrix I need to use... Many thanks for your help Mick -----Original Message----- From: Federico Calboli [mailto:f.calboli at imperial.ac.uk] Sent: 06 April 2005 10:15 To: michael watson (IAH-C) Cc: r-help Subject: RE: [R] Help with three-way anova
On Wed, 2005-04-06 at 09:11 +0100, michael watson (IAH-C) wrote:
OK, so I tried using lm() instead of aov() and they give similar results: My.aov <- aov(IL.4 ~ Infected + Vaccinated + Lesions, data) My.lm <- lm(IL.4 ~ Infected + Vaccinated + Lesions, data)
Incidentally, if you want interaction terms you need lm(IL.4 ~ Infected * Vaccinated * Lesions, data) for all the possible interactions in the model (BUT you need enough degrees of freedom from the start to be able to do this).
If I do summary(My.lm) and summary(My.aov), I get similar results, but
not identical. If I do anova(My.aov) and anova(My.lm) I get identical results. I guess that's to be expected though. Regarding the results of summary(My.lm), basically Intercept, Infected
and Vaccinated are all significant at p<=0.05. I presume the signifcance of the Intercept is that it is significantly different to zero? How do I interpret that?
I guess it's all due to the contrast matrix you used. Check with contrasts() the term(s) in the datafile you use as independent variables, and change the contrast matrix as you see fit. HTH, F
Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com