[R] how to constrast with factorial experiment

From: <szhan_at_uoguelph.ca>
Date: Fri 25 Aug 2006 - 05:41:03 EST


Hello, R users,
I have two factors (treat, section) anova design experiment where there are 3 replicates. The objective of the experiment is to test if there is significant difference of yield between top (section 9 to 11)
and bottom (section 9 to 11) of the fruit tree under treatment. I found that there are interaction between two factors. I wonder if I can contrast means from levels of one factor (section) under another factor (treat)? if so, how to do it in R and how to interpret the output?
Here is the data and commands I used to test the differece between section 1 to 8 and 9 to 11 under treatment. But I don't know if I was right, how to interpret the out and whether there are significant difference between section 1 to 8 and section 9 to 11 under treatment.

yield	replicate	treat	section
35.55	1	Ctl	1
53.70	1	Ctl	2
42.79	1	Ctl	3
434.81	1	Ctl	4
705.96	1	Ctl	5
25.91	1	Ctl	6
57.53	1	Ctl	7
41.45	1	Ctl	8
85.54	1	Ctl	9
51.23	1	Ctl	10
188.24	1	Ctl	11
35.71	2	Ctl	1
45.15	2	Ctl	2
40.10	2	Ctl	3
312.76	2	Ctl	4
804.05	2	Ctl	5
28.22	2	Ctl	6
68.51	2	Ctl	7
46.15	2	Ctl	8
123.14	2	Ctl	9
33.78	2	Ctl	10
121.28	2	Ctl	11
30.96	3	Ctl	1
36.10	3	Ctl	2
47.19	3	Ctl	3
345.80	3	Ctl	4
644.61	3	Ctl	5
27.73	3	Ctl	6
56.63	3	Ctl	7
42.63	3	Ctl	8
61.25	3	Ctl	9
59.43	3	Ctl	10
109.87	3	Ctl	11
143.50	1	Trt	1
82.76	1	Trt	2
125.03	1	Trt	3
493.76	1	Trt	4
868.48	1	Trt	5
45.09	1	Trt	6
249.43	1	Trt	7
167.28	1	Trt	8
274.72	1	Trt	9
176.40	1	Trt	10
393.10	1	Trt	11
93.75	2	Trt	1
63.83	2	Trt	2
117.50	2	Trt	3
362.68	2	Trt	4
659.40	2	Trt	5
62.10	2	Trt	6
218.24	2	Trt	7
210.98	2	Trt	8
291.48	2	Trt	9
209.36	2	Trt	10
454.68	2	Trt	11
119.62	3	Trt	1
66.50	3	Trt	2
87.37	3	Trt	3
414.01	3	Trt	4
707.70	3	Trt	5
44.40	3	Trt	6
142.59	3	Trt	7
137.37	3	Trt	8
181.03	3	Trt	9
131.65	3	Trt	10
310.18	3	Trt	11

> dat1<-read.delim("c:/testcontr.txt", header=T)
> dat1$treat<-as.factor(dat1$treat)
> dat1$replicate<-as.factor(dat1$replicate)
> dat1$section<-as.factor(dat1$section)
> attach(dat1)
> obj<-lm(log2(yield)~treat*section)
> anova(obj)

Analysis of Variance Table

Response: log2(yield)

               Df Sum Sq Mean Sq  F value    Pr(>F)
treat          1 24.608  24.608 297.8649 < 2.2e-16 ***
section       10 99.761   9.976 120.7565 < 2.2e-16 ***
treat:section 10  6.708   0.671   8.1197 2.972e-07 ***
Residuals     44  3.635   0.083
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1


> contrasts(section)<-c(3,3,3,3,3,3,3,3,-8,-8,-8)

> objnew<-lm(log2(yield)~treat*section)
> summary(objnew)
Call: lm(formula = log2(yield) ~ treat * section) Residuals: Min 1Q Median 3Q Max -0.49647 -0.14913 -0.01521 0.17471 0.51105 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 6.288403 0.050034 125.682 < 2e-16 *** treatTrt 1.221219 0.070759 17.259 < 2e-16 *** section1 -0.008502 0.010213 -0.832 0.409675 section2 -0.491175 0.165945 -2.960 0.004942 ** section3 2.569427 0.165945 15.484 < 2e-16 *** section4 3.556067 0.165945 21.429 < 2e-16 *** section5 -1.157069 0.165945 -6.973 1.25e-08 *** section6 -0.003562 0.165945 -0.021 0.982971 section7 -0.487770 0.165945 -2.939 0.005223 ** section8 0.106181 0.165945 0.640 0.525585 section9 -0.776882 0.165945 -4.682 2.74e-05 *** section10 0.759168 0.165945 4.575 3.87e-05 *** treatTrt:section1 -0.049000 0.014444 -3.392 0.001474 ** treatTrt:section2 0.160825 0.234682 0.685 0.496757 treatTrt:section3 -0.949101 0.234682 -4.044 0.000208 *** treatTrt:section4 -1.118870 0.234682 -4.768 2.07e-05 *** treatTrt:section5 -0.295937 0.234682 -1.261 0.213950 treatTrt:section6 0.538638 0.234682 2.295 0.026549 * treatTrt:section7 0.796518 0.234682 3.394 0.001468 ** treatTrt:section8 -0.548744 0.234682 -2.338 0.023984 * treatTrt:section9 -0.191029 0.234682 -0.814 0.420033 treatTrt:section10 -0.556642 0.234682 -2.372 0.022137 * --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 Residual standard error: 0.2874 on 44 degrees of freedom Multiple R-Squared: 0.973, Adjusted R-squared: 0.9601 F-statistic: 75.55 on 21 and 44 DF, p-value: < 2.2e-16 Thanks, Joshua ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Received on Fri Aug 25 05:50:12 2006

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