On Sep 20, 2010, at 11:53 AM, Jabez Wilson wrote:

> Hi, I am trying to reconcile anova table in R (summary(lm)) with

> individual t.test.

> datafilename="

http://personality-project.org/R/datasets/R.appendix1.data
> "

> data.ex1=read.table(datafilename,header=T) #read the data into a

> table

> summary(lm(Alertness~Dosage,data=data.ex1))

The quick answer is that in the ANOVA situation where you are

interpreting individual level parameters, you are testing for the

difference of a particular group from a shared mean (the intercept)

across all three groups, whereas with the t-test you are only

considering two groups at a time. (The default treatment contrasts do

not actually result in the intercept estimate being a global mean,

however.)

--

David.

>

> gives:

>

> Call:

> lm(formula = Alertness ~ Dosage, data = data.ex1)

>

> Residuals:

> Min 1Q Median 3Q Max

> -8.500 -2.437 0.250 2.687 8.500

>

> Coefficients:

> Estimate Std. Error t value Pr(>|t|)

> (Intercept) 32.500 2.010 16.166 6.72e-11 ***

> Dosageb -4.250 2.659 -1.598 0.130880

> Dosagec -13.250 3.179 -4.168 0.000824 ***

> ---

> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

>

> Residual standard error: 4.924 on 15 degrees of freedom

> Multiple R-squared: 0.5396, Adjusted R-squared: 0.4782

> F-statistic: 8.789 on 2 and 15 DF, p-value: 0.002977

>

> As far as I understand it the lines "Dosageb" and "DosageC"

> represent the difference between DosageA and the other two dosages.

> My question is this: are these differences and the p-values

> associated with them the same as a t.test or pairwise.t.test on

> these groups? If I do t.tests, I get different values for t and p-

> value from those in the anova table above.

> Can someone please explain what the discrepancy is?

> Thanks

>

>

>

>

> [[alternative HTML version deleted]]

>

> ______________________________________________

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>

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.

David Winsemius, MD

West Hartford, CT

______________________________________________

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https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide

http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.