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Some Multiple Comparison Procedures III

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Specific Multiple Comparison Procedures III: Tukey HSD and Scheffe Tests

Background

This handout should be read after the introduction to multiple comparison

handouts and the handout on familywise and per comparison error rates. Remember that,

at least in theory, all MC procedures attempt to control familywise Type 1 error rates at

acceptable levels. Thus, its important to be familiar with the concepts of per comparison

and familywise Type 1 error rates.

There are a variety of different approaches to multiple comparisons. In this

handout and in other ones we will discuss several of the major approaches. This handout

will discuss the Tukey HSD (honestly significant difference) and Scheffe approaches to

multiple comparisons. The former test is sometimes called the Tukey WSD (wholly

significant difference) test. I would read this handout after the handouts on the Fisher

LSD and Bonferroni approaches.

The data that we will use to exemplify these tests is the film data weve used

previously. Here it is:

ANGER SAD FEAR HAPPY NEUTRAL

S1 8 9 14 2 12

S2 10 15 16 5 8

S3 7 12 18 7 10

S4 12 13 12 10 4

S5 13 11 10 6 6

MEAN 10.0 12.0 14.0 6.0 8.0

SD 2.55 2.24 3.16 2.92 3.16

We will also need to know that the MSW from the omnibus ANOVA is 8. The F test

from the ANOVA is highly significant: F (4,20) = 6.25, p =.002.

Tukey HSD Test

Overview

The Tukey HSD test can only be used to conduct pairwise comparisons.

Typically, it is used to test all possible pairwise comparisons or to test only some

pairwise comparisons when youve selected them post-hoc. In the latter case, the logic is

that you were only interested in pairwise comparisons before the study began but you had

to look at the data before deciding which pairwise comparisons to actually test. In this

case, the effective field of potential comparisons are all pairwise ones even though

youre only doing some of them. Most commonly, the Tukey HSD test is used to test all

pairwise comparisons. For these purposes it is typically more powerful than the classic

Bonferroni and Scheffe tests. As Ill note below, the comparison to stepdown Bonferroni

is more complex. Let me add a point here. As well see below, you can typically figure

out in advance which of these tests will be more powerful for the particular situation that

youre confronting.

2

Logic and Rationale

The Tukey HSD test has an interesting conceptual basis. Lets assume that we are

only interested in comparing pairs of means (e.g., anger vs. sad), that we have equal

group ns, that the assumptions of the ANOVA are met, and that we want to set our

familywise Type 1 error rate at alpha = .05. If you think about it, one way to control our

FW Type 1 error rate would be to focus on the task of setting the Type 1 error rate for the

largest mean difference at .05. For example, lets assume that the critical t value and

minimum mean difference for all contrasts will be the same (e.g., were using an

approach more like Bonferroni than stepwise Bonferroni). What if we found some

magical critical value that always controlled the Type 1 error rate for the pairwise

contrast with the maximum t or F value at < or = .05? For example, lets assume that the

complete null hypothesis is true (all population means are =) and that we conducted the

film study 1 million times. Each time we ran the 5 film conditions and sampled 25 people

(5 per condition). Lets further say that each time we conducted all 10 pairwise contrasts

and we picked out the maximal contrast. For the particular sample in the table above, that

maximal contrast would be fear-happy. Of course, in other samples, other pairwise

contrasts would be the ones that would be maximal. The idea here is to come up with a

statistical test that protects Type 1 errors even when the contrast tested is always the

maximal contrast. Thus, even though were picking out the contrast each time that is most

likely to be significant, we want to insure that we reject the null hypothesis for this

contrast only 5% of the time.

Thats what the Tukey HSD test does. Its critical values and overall procedure

are designed to control rejection rates of the maximal contrast to the desired alpha level.

Note that if we control the maximal contrast to the desired alpha level, then we

automatically control the familywise error rate to the maximal alpha level given that we

are going to use the same critical t or F value to test all contrasts. Thus, if we fail to reject

the maximal pairwise contrast for a given set of data, then we will automatically fail to

reject any other pairwise contrast. If we fail to reject the maximal contrast 95% of the

time, then we will fail to reject any contrast 95% of the time. Conversely, if we reject the

maximal contrast 5% of the time, our familywise Type 1 error rate can only be 5%. Put

still another way, if ns are equal, it can never happen that we would reject a non-

maximal contrast but fail to reject the maximal contrast: rejection of the latter is a

necessary condition for rejection of the former.

Studentized Range Distribution

As the section above would suggest, the key thing that we need from a

mathematical standpoint is the ability to characterize the sampling distribution of the

maximal contrast. The studentized range (SR) distribution allows us to do this.

The SR distribution is defined as follows. Lets say we generate g independent Z

scores sampled from a normal distribution with a mean of 0 and variance of 1. For

example, we could generate 5 such scores, in which case g = 5. Lets further say that we

compute the absolute value of the difference between each pair of Z scores and that we

pick out the pair thats associated with the biggest difference. Of course, the two Z scores

3

picked out will be the biggest and the smallest. Now, lets also say that we have a chi-

square variable (lets call it V) with degrees of freedom = df that is independent of the Z

scores that we generated. If this is the case, it turns out that the following ratio is

distributed as a studentized range variable (denoted Q).

,

R Max Min

g d f

Z Z

Q

V

df

!

=

(1)

That is, Q is distributed as a studentized range variable with parameters g and df. The

SAS program stud_range1.sas on the web site generates the distribution of the

studentized range distribution for the case in which g=5 and df=45. You can modify this

program to see how the shape changes with different values of g and df.

Given this definition of the S.R. distribution we can further show that the

following test statistic is also distributed as a studentized range variable:

,

, where n = group sample size

R Max Min

g d f

X X

Q

MSW

n

!

= (2)

It time allows, we will show in class that this ratio is in fact distributed as a studentized

range variable. In essence, Q in the equation above is the sampling distribution of the

difference between the biggest and smallest means across an infinite # of samples

assuming the null hypothesis is true. If Q is a sampling distribution in this manner, than

we can use it to test hypotheses concerning the difference between the biggest and

smallest means or, it turns out, between any pair of means. Note that the two parameters

here are g and df and correspond to the # of groups (i.e., # of means involved) and the df

corresponding to the MSW. In addition, of course, you have to specify a given alpha level

(typically .05).

Procedure

When conducting tests using the SR distribution, we will proceed in a manner

similar to the way we proceeded when conducting tests using the t or F distributions. We

will have critical Q value that corresponds to our 5% cutoff point. We will compare our

observed Qs to this critical Q value.

Heres how we proceed. First, we need to find the critical value of the studentized

range distribution that corresponds to the upper 5% of scores of the studentized range

distribution. Thus, we need to make reference to a table of studentized range scores. You

can use the SAS function probmc to do this (well demonstrate this in class).

Alternatively, you can make reference to Table A.4 in Maxwell & Delaney. In the case of

the film data, we would look for the value associated with .05

FW

! = , g = 5, and df=20.

The critical value of Q here is 4.23. Note what the Q critical value of 4.23 represents in

the context of the film study. Assume that the null hypothesis is true (all population

4

means are equal) and we repeated the sampling scheme of the film study an infinite

number of times. Each time, we identify that pairs of means with the maximal difference

and compute an empirical Q using this pair of means. If we plot out the distribution of

obtained Q values, we will find that they will exceed 4.23 5% of the time. Thus, our

critical Q value is indeed our 5% cutoff point.

Once youve got the critical Q value, you can compute the observed Q values

from each pair of means as

A B

Observed

X X

Q

MSW

n

!

=

Here, A and B denote any two groups of interest. You would compare the observed Q to

the critical Q value. If its > crit. Q, you reject the null hypothesis.

Its probably the case, however, that once youve got the critical Q value, the

easiest way to proceed is to compute the minimal mean difference that needs to be

detected to declare the difference significant. Refer to formula (2) above and note that

,

minimum diff *

R

g d f

MSW

X criticalQ

n

=

Thus, for the film data

8

minimum diff 4.23* 5.35

5

X = =

In order for any difference among means to be declared significant, the absolute value of

the difference has to be > 5.35. In the context of the film data, we would find that 3 mean

differences meet this criterion: Fear-happy (dif = 8), fear-neutral (dif = 6), and sad-

neutral (dif = 6). This is the same result we got from the Bonferroni contrasts. However,

note that our minimum mean difference for the Tukey test (5.35) is smaller than the

minimum difference we computed for the Bonferroni test (5.62). If youre going to

conduct all pairwise contrasts on means, the Tukey test is more powerful than the

Bonferroni test.

The choice between Tukey and stepdown Bonferroni is more complicated. The

first step in stepdown Bonferroni (difference between largest and smallest means) is

identical to the first step in the traditional (non-step-down) Bonferroni test. Thus, at this

step we favor Tukey. Note, though, how with each succeeding step, the critical t or F

value for stepdown Bonferroni gets smaller and smaller (youre dividing .05 by a smaller

number). The Tukey value stays constant across all comparisons. Typically, there is a

point in the sequence at which stepdown Bonferroni becomes more powerful than Tukey.

Thus, for early comparisons in the sequence (comparisons involving bigger differences

among means), Tukey is more powerful and desirable, but for later comparisons,

stepwise Bonferroni is more desirable. On balance, I would probably choose Tukey

simply because if the first step is not significant with stepwise Bonferroni, you cant

declare any contrasts to be significant.

5

From a more conceptual perspective, heres the key thing to understand. Our

critical Q of 4.23 and our minimal mean difference of 5.36 originate in the attempt to

control Type 1 errors for the maximal contrast. That is, if the null hypothesis is true, we

only want to declare the 2 maximally different means to be significantly different 5% of

the time. However, you should recognize that in the process we also control the

familywise Type 1 error rate for the whole set of pairwise contrasts at alpha = .05. The

reasons are: (1) Under the complete null hypothesis, if we use this procedure the maximal

contrast will not be significant 95% of the time; and, (2) if the maximal contrast is not

significant using the Tukey procedure, theres no way any other contrasts can be

significant. Thus, if the null hypothesis is true, 95% of the time we will judge no contrasts

to be significant using the Tukey HSD test.

The SAS program film_cont_tukey.sas that is on the web site shows you how to

conduct Tukey HSD contrasts using SAS. You will see that the output using the means

command makes more intuitive sense than the output using the lsmeans command. I will

explain the latter output in class.

Let me also note that the Tukey procedure assumes both equal ns and

homogeneity of population variances. In the unequal-n case, the Tukey-Kramer test can

be used. This test is discussed in Maxwell & Delaney pp. 184-185. For violations of

homogeneity of variance, neither Tukey procedure is appropriate but there are

alternatives available that are quite similar to the Welch ADF omnibus test that we have

discussed. See the Maxwell & Delaney discussion on pp. 145-150 and 184-5.

Scheffe Test

Overview

The Scheffe MCP can be used to test any contrast or set of contrasts:

whether they are pairwise or complex. In my view, it is the only true post-hoc contrast. In

essence, it is appropriate for the case where the researcher is willing initially to consider

any possible contrast or set of contrasts without being able to specify in advance which

specific contrasts he or she wants to do. Instead after looking at the data, the researcher

decides to do a contrast or contrasts. This might sound like an unrealistic situation to you

and it probably is. However, it is important that there be a MCP procedure that helps

control familywise error rates for truly post-hoc, exploratory type situations. If youre not

in that situation, the typical advice is dont do a Scheffe test. The reason is that, relative

to other procedures, it has low power. Given the tradeoff between Type 1 errors and

power, low power for the Scheffe test should make sense. This test is designed to control

Type 1 errors even if the family of contrasts conducted was infinite in size. For example,

in the context of the film data, there are only 10 pairwise contrasts that one could

conduct. However, if one considered both pairwise and complex contrasts, there literally

is an infinite # of possibilities. A truly post-hoc procedure needs to protect familywise

error rates even if the family were infinitely large or, more realistically, if any of the

infinite number of contrasts were selected by the researcher. One would expect that such

a procedure would be associated with per comparison Type 1 error rates that are quite

low.

6

Let me note, however, that there are actually instances in which the Scheffe test is

more powerful than other MCPs. In particular, this test can be more powerful than the

classic Bonferroni test under some circumstances. I will discuss this point below

Logic and Procedure

The Scheffe test has an underlying logic that is similar to that of the Tukey HSD

test and is actually quite nifty. Recall how the latter controls familywise Type 1 error

rates for all pairwise contrasts by controlling the Type 1 error rate for the maximal

pairwise contrast. The Scheffe procedure has a similar logic except now the goal is to

control familywise Type 1 error rates for any set of contrasts (pairwise and/or complex)

of any size. It does this by controlling the Type 1 error rate for the maximal contrast that

one could possibly observe. Note that were not just thinking about the maximal pairwise

contrasts here. Were thinking about the maximal contrast of any type.

You might ask: if there are an infinite # of potential contrasts, how on earth

would we ever be able to identify the contrast with the largest value? Wouldnt that

contrast vary appreciably from sample to sample or study to study? Well it turns out that

we know what the maximal contrast will always be. I will present the results here and

refer you to the discussion in Maxwell and Delaney (pp. 186-192) to further flesh out the

proofs and underlying rationale if youre interested.

When we conduct Scheffe contrasts, we typically think in terms of Fs rather than

ts. Recall from an earlier handout that when we test a contrast as an F distribution

2

2

1

,

j

j

j

SS

F where

MSW

SS

c

n

"

"

"

=

=

=

"

!

It follows that the largest F value we could observe would be linked to the contrast with

the largest SS. In other words,

max

maximum

SS

F

MSW

=

As shown in Maxwell & Delaney, we can show that the SS for any contrast must always

be # the SS Between from the omnibus ANOVA. That is,

SS SSB " #

We can further show that it is in fact possible to identify a contrast whose value is

identical to the SSB. This contrast has the following coefficients:

7

( )

j j j

c n Y Y = !

As shown in footnote 6 in M&D on p. 764, a contrast with these coefficients will always

= the SSB. The point here is not that ( )

j j j

c n Y Y = ! is an attractive or meaningful

contrast that you should use. Rather, the point is that SS for the maximal contrast possible

is indeed = SSB. In other words, we now know that:

maximum

SSB

F

MSW

=

However, we also know that:

( 1) , where J = # of groups SSB J MSB = !

Thus, by substitution:

max

( 1)

( 1)*

imum

J MSB

F

MSW

MSB

J

MSW

!

=

= !

(3)

Now, consider equation (3) above. Lets assume the null hypothesis is true. We know that

under the null hypothesis

MSB

MSW

is distributed as a central F variable with (J-1) and (N-J)

degree of freedom. It follows from (3) that

maximum

F -- the value of the maximum contrast

is distributed as J-1 times a central F variable. That is, lets assume that the null

hypothesis is true (all population means are equal). We do a million experiments and for

each experiment we the maximal contrast --- the one where the coefficients are

( )

j j j

c n Y Y = ! . This contrast is distributed as J-1 times an F variable. If we want to find

the upper 5% cutoff point for this contrast, we: (1) find the upper 5% cutoff point for a

central F distribution with J-1 and N-J df (denote this

,.05, 1, crit J N J

F

! !

); and, (2)multiply this

cutoff point by J-1 (i.e., compute (J-1)*

,.05, 1, crit J N J

F

! !

). The result is the upper 5% critical

value (= cutoff point) for the maximal contrast. This is the critical value that we will use

when we do Scheffe contrasts.

The logic here is similar to that for the Tukey test. The key point is that by

holding Type 1 errors for the maximal contrast to the desired alpha level, we hold the

familywise error rate for any family of contrasts to that desired alpha level. The insight

here is that if we reject the null hypothesis for the maximal possible contrast only 5% of

the time, our familywise Type 1 error rate can not be > .05.

8

The logic here reveals another interesting point. An observed value of a Scheffe

contrast is significant if it exceeds the 5% cutoff point = (J-1)*

,.05, 1, crit J N J

F

! !

. The

ANOVA is significant only if its F value exceeds

,.05, 1, crit J N J

F

! !

. There is a 1-to-1 relation

here. The ANOVA is significant only if the maximal contrast as tested by Scheffes

method is significant and the maximal contrast as tested by Scheffes method is

significant only if the ANOVA is significant. A significant ANOVA tells us, then, tells us

that at least one contrast is significant.

Heres how we proceed when doing Scheffes comparisons:

(1) We compute (J-1)*

,.05, 1, crit J N J

F

! !

. This is our upper 5% critical value

(2) We compute our observed contrasts and F values of interest using the

standard formulae:

2

2

1

j

j j

Observed

SS

c

n

SS

F

MSW

"

"

"

=

=

=

"

!

(3) We compare our observed F computed in step 2 to the critical F

computed in step 1. If

Observed Crit

F F > , we reject the null hypothesis and

declare the contrast significant.

So, lets take the film data as an example. Well just do one contrast to exemplify the

procedure. Lets say that we want to compare sad ( 12

SAD

Y = ) to happy ( 6

Happy

Y = ):

.05,4,20

Crit

(1) We need to find our critical F.

We see that 2.867 from a table of F values.

Thus, F for our contrast = (J-1)*2.867= 4*2.867=11.47

F =

(2) We compute the observed value of our contrast

9

2

2

1

2

(12 6)

1 1

( )

5 5

36

2

5

90

j

j j

SS

c

n

"

"

=

=

!

=

+

=

=

"

!

(3) We compute our observed F

90

8

11.25

Observed

SS

F

MSW

"

=

=

=

(4) We compare the observed to the critical F. Here we see that 11.25 < 11.47. Thus, we

fail to reject the null hypothesis that sad and happy differ.

Note that when we did Bonferroni and Tukey contrasts, we found that sad and happy did

significantly differ. The Scheffe contrast is associated with relatively low power when

compared to other procedures.

One could also compute a Scheffe complex contrast using a similar procedure

If we considered conducting a Scheffe test for a set of pairwise contrasts, one thing that

we could do is compute the minimum mean difference necessary for the contrast to be

significant.

10

2

2

2

To do this, we set:

Thus,

* * min. mean diff.

j

j j

Crit

j

Crit A B

j

j

c

n

F

MSW

c

F MSW Y Y

n

"

"

=

= ! = =

"

"

In the context of the film data, then

2

min. mean dif = 11.47*8*( ) 6.06

5

=

Thus, for any mean difference to be declared significant, it has to be greater than 6.06.

Note how this min. mean difference is greater than those for the Bonferroni or Tukey

HSD tests comparing all pairs of means:

Test Minimum Mean Difference

Bonferroni 5.64

Tukey 5.35

Scheffe 6.06

Clearly, we would not choose the Scheffe test over these procedures in this case.

This test, in essence, is typically a last resort. It is used when at least one of the contrasts

that you are doing was not anticipated in advance and is based on post-hoc peeking at

the data.

You should note, however, that when youre doing a large number of contrasts

(and particularly when youre doing so when ns and df are very small) the critical values

for the classic Bonferroni test (non-step-down) can actually be greater than those for the

Scheffe. Thus, the latter can be more powerful than the former. In this regard, recall that

the Scheffe critical value stays constant across variations in the # of contrasts actually

performed, while Bonferroni critical values go up (and per comparison alphas go down)

as you add contrasts. For example, if you have 5 groups and 20 df (as we do in the film

study) and you 18 contrasts (!), youd be better off doing Scheffes than Bonferroni.

Table 5.5 in Maxwell & Delaney offers a nice summary of when to use Bonferroni rather

than Scheffe. I suspect that for situations you actually encounter in practice youll want to

do Bonferroni contrasts rather than Scheffes. Moreover, youll probably want to do

stepdown Bonferronis most of all.

11

Note that if the choice is stepdown Bonferroni vs. Scheffe, youre typically going

to have greater power overall with the former. In those cases whether the Table 5.5

indicates that Scheffe is better than traditional Bonferroni, the choice is more complex.

For the first contrast you conduct (the one with the biggest value), Scheffe is more

powerful than both traditional Bonferroni and stepwise Bonferroni . At a certain point in

the stepdown sequence, however, the stepdown Bon will become more powerful.

Let me emphasize, though, that this whole discussion of Bonferroni vs. Scheffe

presumes that you have identified the contrasts that you want to use in advance. If you

are truly picking comparisons to do on a post-hoc basis, you should use Scheffe no matter

what the # of contrasts youre doing.

The SAS program film_cont_scheffe.sas demonstrates how to do Scheffe

contrasts using SAS.

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