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Jun Shen

2009-Aug-19 21:33 UTC

[R] Contrasts within ANOVA frame (Repost)

Would like to try my luck to see if I can catch your eyes.

I was trying to do some contrasts within ANOVA. I searched the archive and
found a clue posted by Steffen Katzner
( http://tolstoy.newcastle.edu.au/R/help/06/01/19385.html)

I have three levels for a factor names "StdLot" and want to make three
comparisons, 1 vs 2, 1 vs 3 and 2 vs 3.

First,
contrasts(d3$StdLot,3)<-matrix(c(1,-1, 0,0,1,-1,1,0,-1),3,3)   #d3 is the
data set. set up the contrast matrix

Second,
aov(Bkg~StdLot,na.rm=T,data=d3,contrasts=contrasts(d3$StdLot))->mod.aov
#ANOVA,

Finally,
summary(mod.aov,split=list(StdLot=list('1 vs 2'=1,'2 vs
3'=2,'1 vs 3'=3)))
#comparison summary

Here is the final result I got, the third comparison is missing. Does anyone
have any idea what is wrong here? If I change the order of the comparisons
it's always the third one missing.  So I guess it's not due to the data.
Appreciate any comment.

                  Df Sum Sq Mean Sq F value    Pr(>F)
StdLot             2  1.905   0.953 10.3769 3.710e-05 ***
  StdLot: 1 vs 2   1  0.223   0.223  2.4239    0.1200
  StdLot: 2 vs 3   1  1.683   1.683 18.3299 2.162e-05 ***
  StdLot: 1 vs 3   1
Residuals        601 55.173   0.092
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2 observations deleted due to missingness


-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

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Mark Difford

2009-Aug-20 08:24 UTC

head link

[R] Contrasts within ANOVA frame (Repost)

Hi Jun,
>> I have three levels for a factor names "StdLot" and want to
make three
>> comparisons, 1 vs 2, 1 vs 3 and 2 vs 3.
With only three levels to your factor, the contrast matrix you are
specifying is over-parametrized (i.e. over-specified): it has 3 rows and 3
columns.

## Look at the default behaviour
contrasts(d3$StdLot) <- NULL
contrasts(d3$StdLot)

contrasts(d3$StdLot) <- contr.helmert
contrasts(d3$StdLot)

I think what you really want are linear contrasts, which you will find in
package car (?linear.hypothesis), in gmodels (?estimable) [based on Frank
Harrell's approach; so look at his package Design], and package multcomp,
amongst others.

Regards, Mark.


Jun Shen-3 wrote:> 
> Would like to try my luck to see if I can catch your eyes.
> 
> I was trying to do some contrasts within ANOVA. I searched the archive and
> found a clue posted by Steffen Katzner
> ( http://tolstoy.newcastle.edu.au/R/help/06/01/19385.html)
> 
> I have three levels for a factor names "StdLot" and want to make
three
> comparisons, 1 vs 2, 1 vs 3 and 2 vs 3.
> 
> First,
> contrasts(d3$StdLot,3)<-matrix(c(1,-1, 0,0,1,-1,1,0,-1),3,3)   #d3 is
the
> data set. set up the contrast matrix
> 
> Second,
> aov(Bkg~StdLot,na.rm=T,data=d3,contrasts=contrasts(d3$StdLot))->mod.aov
> #ANOVA,
> 
> Finally,
> summary(mod.aov,split=list(StdLot=list('1 vs 2'=1,'2 vs
3'=2,'1 vs 3'=3)))
> #comparison summary
> 
> Here is the final result I got, the third comparison is missing. Does
> anyone
> have any idea what is wrong here? If I change the order of the comparisons
> it's always the third one missing.  So I guess it's not due to the
data.
> Appreciate any comment.
> 
>                   Df Sum Sq Mean Sq F value    Pr(>F)
> StdLot             2  1.905   0.953 10.3769 3.710e-05 ***
>   StdLot: 1 vs 2   1  0.223   0.223  2.4239    0.1200
>   StdLot: 2 vs 3   1  1.683   1.683 18.3299 2.162e-05 ***
>   StdLot: 1 vs 3   1
> Residuals        601 55.173   0.092
> ---
> Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
> 2 observations deleted due to missingness
> 
> 
> -- 
> Jun Shen PhD
> PK/PD Scientist
> BioPharma Services
> Millipore Corporation
> 15 Research Park Dr.
> St Charles, MO 63304
> Direct: 636-720-1589
> 
> 	[[alternative HTML version deleted]]
> 
> 
> ______________________________________________
> R-help at r-project.org 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.
> 
> 
-- 
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JLucke at ria.buffalo.edu

2009-Aug-20 13:55 UTC

head link

[R] Contrasts within ANOVA frame (Repost)

Dr Shen

Even though you pose 3 contrasts, there are only 2 degrees of freedom as 
the 3rd contrast is the sum of the first two.  Your aov output states this 
as StdLot has only 2 df.  Having used up your df, the aov has nothing to 
report.

Joe

Joseph F. Lucke
Senior Statistician
Research Institute on Addictions
State University of New York at Buffalo
1021 Main Street
Buffalo, NY  14203-1016
Office: 716-887-6807
Fax:     716-887-2510
http://www.ria.buffalo.edu/profiles/lucke.html




Jun Shen <jun.shen.ut@gmail.com> 
Sent by: r-help-bounces@r-project.org
08/19/2009 05:33 PM

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r-help@r-project.org
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Subject
[R] Contrasts within ANOVA frame (Repost)






Would like to try my luck to see if I can catch your eyes.

I was trying to do some contrasts within ANOVA. I searched the archive and
found a clue posted by Steffen Katzner
( http://tolstoy.newcastle.edu.au/R/help/06/01/19385.html)

I have three levels for a factor names "StdLot" and want to make three
comparisons, 1 vs 2, 1 vs 3 and 2 vs 3.

First,
contrasts(d3$StdLot,3)<-matrix(c(1,-1, 0,0,1,-1,1,0,-1),3,3)   #d3 is the
data set. set up the contrast matrix

Second,
aov(Bkg~StdLot,na.rm=T,data=d3,contrasts=contrasts(d3$StdLot))->mod.aov
#ANOVA,

Finally,
summary(mod.aov,split=list(StdLot=list('1 vs 2'=1,'2 vs
3'=2,'1 vs 3'=3)))
#comparison summary

Here is the final result I got, the third comparison is missing. Does 
anyone
have any idea what is wrong here? If I change the order of the comparisons
it's always the third one missing.  So I guess it's not due to the data.
Appreciate any comment.

                  Df Sum Sq Mean Sq F value    Pr(>F)
StdLot             2  1.905   0.953 10.3769 3.710e-05 ***
  StdLot: 1 vs 2   1  0.223   0.223  2.4239    0.1200
  StdLot: 2 vs 3   1  1.683   1.683 18.3299 2.162e-05 ***
  StdLot: 1 vs 3   1
Residuals        601 55.173   0.092
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2 observations deleted due to missingness


-- 
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589

                 [[alternative HTML version deleted]]

______________________________________________
R-help@r-project.org 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.



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