[R] ANOVA contrast matrix vs. TukeyHSD?
Sam Yeaman
yeaman at zoology.ubc.ca
Wed Sep 17 22:57:40 CEST 2008
Dear Help List,
Thanks in advance for reading...I hope my questions are not too ignorant.
I have an experiment looking at evolution of wing size [centroid] in
fruitflies and the effect of 6 different experimental treatments
[treatment]. I have five replicate populations [replic] in each
treatment and have reared the flies in two different temperatures [cond]
to assay the wing size, making measurements on males and females
[gender]. My design can be summarized as follows:
This is my model (I think it's right, ignoring interaction terms for
simplicity):
> lm1 ~ aov (centroid ~ gender + cond + treatment/replic, data = parents)
The treatments are:
> levels (parents$treatment)
[1] "c" "h" "mc" "mh" "s" "t"
I only care about a few of the pairwise comparisons between the levels
of "treatment", as only certain contrasts are scientifically interesting:
c vs. h
mh vs. mc
(c + h) vs. s [I would like to compare the mean of c and h (my
controls) to s and t)
(c + h) vs. t
s vs. t
h vs. mh
c vs. mc
These are two more than I can specify using "contrasts()" and they are
not orthogonal. I can use the TukeyHSD and only look at the comparisons
I care about, but I think this should give me much less power than
specifying a few a priori contrasts (?). Also, I don't know how to
combine my controls (c + h) into a single comparison using TukeyHSD.
My first problem is that when I specify the matrix shown below (the
first 5 comparisons from above), I get a much higher p-value on some of
the planned contrasts than I do on the TukeyHSD:
contrasts (parents$treatment) <- cbind
(c(-1,1,0,0,0,0),c(-1,-1,0,0,2,0),c(-1,-1,0,0,0,2),c(0,0,-1,1,0,0),c(0,0,0,0,1,-1))
> contrasts(parents$treatment)
[,1] [,2] [,3] [,4] [,5]
c -1 -1 -1 0 0
h 1 -1 -1 0 0
mc 0 0 0 -1 0
mh 0 0 0 1 0
s 0 2 0 0 1
t 0 0 2 0 -1
#### THE OUTPUT (truncated) ####
Call:
lm(formula = centroid ~ gender + cond + treatment/replic, data = parents)
Residuals:
Min 1Q Median 3Q Max
-81.58846 -4.53540 0.00803 4.76568 39.84177
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) 328.73096 0.26303 1249.770 < 2e-16 ***
genders -37.39069 0.19661 -190.179 < 2e-16 ***
condu -37.47740 0.19693 -190.308 < 2e-16 ***
treatment1 0.51026 0.40084 1.273 0.203079
treatment2 -0.17333 0.23175 -0.748 0.454541
treatment3 0.07761 0.22535 0.344 0.730566
treatment4 -1.96020 0.38524 -5.088 3.73e-07 ***
treatment5 NA NA NA NA
###### The TukeyHSD output (truncated) #####
Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = centroid ~ gender + cond + treatment/replic, data =
parents)
*
*
*
$treatment
diff lwr upr p adj
h-c -1.38085941 -2.382732615 -0.3789862 0.0012123
mc-c -2.22026936 -3.198423972 -1.2421147 0.0000000
mh-c -2.27157901 -3.268013478 -1.2751445 0.0000000
s-c -1.19540471 -2.170272952 -0.2205365 0.0063382
t-c -0.39899955 -1.374954044 0.5769549 0.8533107
mc-h -0.83940995 -1.813993060 0.1351732 0.1378366
mh-h -0.89071960 -1.883648319 0.1022091 0.1081954
s-h 0.18545470 -0.785829956 1.1567394 0.9943136
t-h 0.98185986 0.009484949 1.9542348 0.0462121
mh-mc -0.05130965 -1.020300865 0.9176816 0.9999892
s-mc 1.02486465 0.078064558 1.9716647 0.0249356
t-mc 1.82126980 0.873351301 2.7691883 0.0000007
s-mh 1.07617430 0.110500644 2.0418480 0.0187007
t-mh 1.87257946 0.905809220 2.8393497 0.0000005
t-s 0.79640515 -0.148121782 1.7409321 0.1550137
When I specify the c vs. h comparison, I am getting a p-value of
0.203079, but the TukeyHSD gives the same contrast a p-value of
0.0012123. Also, the fifth comparison gives "NA"; I assume this is due
to it being non-orthogonal? I feel like I am either misunderstanding the
point of contrasts() completely or I have done something wrong, so I
would really appreciate any help.
My other question is related...just wondering why I need to limit myself
to only orthogonal comparisons using contrasts()? This eliminates
comparisons of scientific interest, for example if c vs. h, mc vs. c,
and mh vs. h are all different, I have no way of knowing if mc vs. mh is
significantly different by examining the other contrasts.
Sorry if these questions are ignorant...I have spent a long time trying
to figure it out and haven't found the answer in either the available
books or the help list.
Many thanks,
Sam Yeaman
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