Anova 2aw

Psych. Statistics: Two way analysis of variance (ANOVA).
Page 1 of 24
Analysis of Variance - Two Way

I. Introduction
1. Design
2. The Notion of an Interaction
3. Advantages of the Factorial Design
II. Notation
III. Logic
IV. Formal Example
1. Research Question
2. Hypotheses
3. Assumptions
4. Decision Rules
5. Computation - [Minitab]
6. Decision
V. Comparisons Revisited
Practice Problems (Answers)

Homework
I. Introduction
In addition to being able to analyze an experiment with one Independent Variable (IV), the ANOVA can be used for
factorial designs (or designs which employ more than one IV). Note that, in this context, an IV is often referred to as a
factor. The factorial design is very popular in the social sciences. It has a few advantages over single variable designs.
The most important of these is that it can provide some unique and relevant information about how variables interact or
combine in the effect they have on the DV.
Let's look at these design issues in more detail with a concrete example and then consider the unique information that
this design provides.
1. Design
Our example involves the effects of maternal consumption of ethanol on the behavior of the offspring of rats. The
human literature had shown that children diagnosed with Fetal Alcohol Syndrome (FAS) were more active and
impulsive than children not receiving this diagnosis. They also seemed to have a more difficult time controlling
themselves (i.e., self restraint). These problems typically become less severe as the child ages.
The human literature is difficult to interpret however, because questions remain as to the cause and effect
relationships involved. Were the behavioral abnormalities observed in the children with FAS due to the fact that
their mothers consumed alcohol while they were pregnant? Or, were the abnormalities observed due to nutritional
factors (since the diet of an alcoholic is typically not wholesome & well balanced)? Another possible causal factor
of the abnormalities observed is spousal abuse.
Ethically, we cannot conduct the experiments necessary to determine the causal relations involved in humans.
Thus, the experiment that will serve as our example employed rats as subjects (based on Riley, Lockrey &
Shapiro, 1979). Earlier literature had demonstrated that rats can be used as an animal model of FAS. Offspring of
rodents given alcohol when pregnant show similar morphological and behavioral changes to that observed in
humans.
So, we will have two IVs or factors and each will have two levels (or possible values). The table below illustrates
http://www4.uwsp.edu/psych/stat/13/anova-2w.htm 9/1/2012
Psych. Statistics: Two way analysis of variance (ANOVA). Page 2 of 24
the design. Note that EDC refers to Ethanol Derived Calories.
Age (factor B)
Adolescent Adult
Chocolate
Milk n=5 n=5
Maternal (0% EDC)
Diet White
(factor A) Russian n=5 n=5
(35% EDC)
This is an example of a 2x2 factorial design with 4 groups (or cells), each of which has 5 subjects. This is
the simplest possible factorial design. The DV used was a Passive Avoidance (PA) task. Rats are nocturnal,
burrowing creatures and thus, they prefer a dark area to one that is brightly lit. The PA task uses this
preference to test their learning ability. The apparatus has two compartments separated by a door that can
be lifted out. One of the compartments has a light bulb which is controlled by the experimenter.
Furthermore, the floor can be electrified. In this case, the rat receives a brief, mild electric shock. Finally,
there is also a holding cage (separate from the experimental apparatus) available.
The learning takes place over a series of trials. The first trial goes something like this: The rat is placed in
the compartment with the light bulb as shown below.
When the trial begins, three things happen. The door is raised, the light is turned on, and a stopwatch is
started (see the diagram below).
Within a few seconds of the door being raised, the rat will typically sniff around and begin to move into the
darker compartment (without the light). When the rat has completely entered the darker compartment, the
door is closed and the brief, mild shock is administered. The goal is for the rat to learn not to move into the
darker compartment. In other words, by remaining passive, the rat can avoid the shock, hence the term
passive avoidance. For our purposes, we will use a criteria of 180 seconds as our operational definition of
learning PA. That is, when the rat remains in the brightly lit compartment for 3 minutes, we will say that it
has learned the task and what we measure is the number of trials it takes the rat to do this. (Note that a
"smart" rat will take less trials to learn.) Thus, the PA task was chosen as the DV because it can be thought
of as a measure of "self restraint."
Now let's discuss the types of information this design can yield. There are three types:
Factor A - addresses whether maternal diet effects PA learning.

Factor B - addresses whether age is related to PA learning.
AxB Interaction - addresses whether the effects of maternal diet depend on the age of the offspring.
More generally, we speak of several kinds of effects:
Treatment Effect - a difference in population means. There are two kinds:

1. Main Effect - a difference in population means for a factor collapsed over the levels of all
other factors in the design.
2. Interaction Effect- occurs when the effect on one factor is not the same at the levels of
another.
Thus a two way factorial design tells us about two main effects and the interaction.
2. The Notion of an Interaction
Let's consider all of the possible outcomes that could occur in the example introduced above. This will help us to
better understand the effects involved in general and the concept of an interaction in particular. There are eight
possibilities for what could occur. In other words, there are eight possibilities of what could be significant in the
analysis. That is:
1. Nothing
2. Main effect of factor A
3. Main effect of factor B

4. Both main effects (factors A and B)
5. A x B interaction
6. A x B interaction and main effect of factor A
7. A x B interaction and main effect of factor B
8. A x B interaction and both main effects (factors A and B)
Let's consider each of these possibilities in detail. We'll present the means in a table along with the marginal
means (which make the main effects easier to see) as well as in the format of a figure. For this educational
exercise, we need to make a silly assumption so that we won't have to deal with raw data and computational
analysis. We will assume that a difference in means of two trials is significant. Normally we would need the
raw data and have to perform the statistical computations to determine what is significant. To save lots of time
and be able to concentrate on the important ideas involved, we will go with this arbitrary and silly assumption of a
two trial difference necessary for statistical significance.
1. The first possibility is that nothing is significant. Here is one possible representation of this outcome.
Age (factor B) A
Adolescent Adult marginals
Maternal Diet (0% EDC) 3 3 3
(factor A) (35% EDC) 3 3 3
B marginals 3 3
The fact that neither the cell means nor the marginal means show any differences tell us that nothing is
significant. In graphical form:
2. The second possibility is that the main effect of factor A is significant. Here is one possible
representation of this outcome.
Age (factor B) A
(factor A) (35% EDC) 4 4 4

B marginals 3 3
Notice that the A marginals show a difference of two and thus the main effect of factor A is significant. The
animals receiving alcohol in utero took more trials to learn PA than controls. The fact that the effect is
consistent across both levels of factor B tells us that there is no interaction. In graphical form:
3. The next possibility is that the main effect of factor B is significant. Here is one possible representation
of this outcome.
Age (factor B) A
(factor A) (35% EDC) 4 2 3
B marginals 4 2
Notice that the B marginals show a difference of two and thus the main effect of factor B is significant. The
older animals took fewer trials to learn PA than the younger animals. The fact that the effect is consistent
across both levels of factor A tells us that there is no interaction. In graphical form:
4. The next possibility is that both main effects are significant. Here is one possible representation of this
outcome.
Age (factor B) A

(factor A) (35% EDC) 5 3 4
B marginals 4 2
Notice that both sets of marginals show a difference of two and thus main effects are significant. The
animals receiving alcohol in utero took more trials to learn PA than controls and the older animals took less
trials to learn PA than the younger animals. The fact that both of these main effects are consistent across the
levels of the remaining factor tells us that there is no interaction. In graphical form:
5. The next possibility is that the interaction is significant. Here is one possible representation of this
outcome.
Age (factor B) A

(factor A) (35% EDC) 4 2 3
B marginals 3 3
Notice that both sets of marginals show no difference, thus neither main effect is significant. However,
some of the cell means do differ by two. The animals receiving alcohol in utero took more trials to learn PA
when young and less when older than controls. In other words, the effects of prenatal alcohol depended on
the age of the animal when tested. Whenever the effect of one factor depends upon the levels of another,
there is an interaction. In graphical form:
6. The next possibility is the interaction and the main effect of factor A are significant. Here is one possible
Age (factor B) A
(factor A) (35% EDC) 5 3 4
B marginals 3 3
Notice that the B marginals show no difference, thus the main effect of B is not significant. The A
marginals do show a difference of two which demonstrates a main effect of factor A. This tells us that the
animals that received alcohol in utero took longer to learn PA than the animals that didn't. However, the cell
means tell the real story here. That is, the effect depends on age. The animals receiving alcohol in utero
took more trials to learn PA when young but were normal when older when compared to controls. In
graphical form:
One famous statistician (Keppel) has noted something to the effect that when there is an interaction along
with main effects, we must reexamine the main effects to see if they are really worth paying attention to. In
other words, an interaction can override any main effects. Thus, let us reexamine the main effect in the
present case. It says that animals that received alcohol in utero took longer to learn PA than the animals that
didn't. However, when looking at the cell means we see that this is only the case for the younger animals.
Thus, in this case, the interaction overrides the main effect. In other words, it gives us a more accurate
picture of what is actually occurring.
7. The next possibility is that the interaction and main effect of factor B are significant. Here is one possible
Age (factor B) A

(factor A) (35% EDC) 5 1 3
B marginals 4 2
Notice that the A marginals show no difference, thus the main effect of A is not significant. The B
marginals do show a difference of two which demonstrates a main effect of factor B. This tells us that
younger animals took longer to learn PA than older animals. However, the cell means tell the real story
here. That is, the improvement with age only occurs for animals receiving alcohol in utero. In graphical
form:
Given that there is an interaction along with a main effect, we must reexamine the main effect to see if it is
worth paying attention to. The main effect says that older animals learn more quickly than young ones.
However, when looking at the cell means we see that this is only the case for animals receiving alcohol in
utero. Thus, in this case, the interaction overrides the main effect.
8. The next possibility is that the interaction and both main effects are significant. Here is one possible
Age (factor B) A

(factor A) (35% EDC) 5 1 3
B marginals 3 1
The main effect of A (seen in the A marginals as usual), tells us that the animals receiving alcohol in utero
took more trials to learn than controls. The main effect of factor B tells us that adults learned more quickly
than younger animals. However, the cell means tell the real story here. That is, the interaction tells us that
the effect of alcohol depended upon age. For the younger animals, animals receiving alcohol in utero
showed impaired learning compared to controls while this deficit was not observed in adults. In graphical
form:
Given that there is an interaction along with the main effects, we must reexamine the main effects to see if
they are really worth paying attention to. The main effect of factor A says that animals receiving alcohol in
utero showed impaired learning compared to controls. However, the cell means (i.e., the interaction) show
that this is not always the case. The main effect of factor B says that adults learned more quickly than
younger animals, but this too is not always the case. Thus, the interaction is what is important here. By the
way, this outcome is in essence what the investigators actually observed.
At this point, you might be wondering if there is ever a situation where a main effect and interaction are
significant and the main effect is still worth paying attention to. The diagram below presents such a
scenario.
In this case, there is a main effect of factor A (maternal ethanol) and an interaction. The main effect says
that animals receiving alcohol in utero took more trials to learn than controls. Even though the interaction
(which says that the effect is greater in young animals) is significant, the main effect is also worth paying
attention to because it holds true at all levels of factor B.
3. Advantages of the Factorial Design
There are three important advantages to the factorial design:
1. Economy
The design provides more information from the same amount of work. Consider the effects of
marijuana on memory. We have an experimental group that receives the drug and a control group that
receives a placebo.
Two Group Design Factorial Design

Control Experimental Control Experimental
n=10 n=10 naive n=5 n=5
experienced n=5 n=5
n=10 n=10
Although the number of subjects is the same in both designs, with the factorial design, we
obtain the additional information about the relationship of previous experience with the drug to
memory performance.
2. Experimental Control & Increased Generality of the Results
Suppose we are interested in the effects of teaching method on student performance. A potential
extraneous variable in this case is the IQ of the students. The EV inflates the error term (i.e., the
within group variability). One way to deal with this problem is to employ subjects with a
homogeneous IQ. A more elegant solution is to include IQ as a factor in the design and thus remove
this added source of variability from the error term.
Teaching Method
A B C
Low
IQ Medium
High
An additional potential advantage of this approach is that the results have more generality (they
apply to folks of varying IQs).
3. The Interaction
The factorial design is the only way that we can investigate the interactions among IVs. This is
particularly important because the effect of an IV rarely occurs in isolation. In the real world, many
variables operate simultaneously. Thus, the factorial design allows us to investigate these more
realistic situations.
In the two way factorial design, there is one possible interaction. We have discussed the notion of the
interaction in detail above. In a three way factorial design, there are four possible interactions, that is:
A x B, A x C, B x C, and the triple interaction, A x B x C. Triple interactions are beyond the scope of
this course and thus will not be discussed further.
II. Notation
We already knew that:
Any Last
Score i n
Factor A j p
Factor B k q only thing new
So p equals the number of levels of factor A and q equals the number of levels of factor B.
Thus:
Factor B
A
b1 b2 bk bq Marginals
a1 Xi11 Xi12 Xi1k Xi1q
Xn11 Xn12 Xn1k Xn1q
a2 Xi21 Xi22 Xi2k Xi2q
Xn21 Xn22 Xn2k Xn2q
aj Xij1 Xij2 Xijk Xijq

Xnj1 Xnj2 Xnjk Xnjq
Factor
A
ap Xip1 Xip2 Xipk Xipq

Xnp1 Xnp2 Xnpk Xnpq
B
Marginals
Grand Mean
So, a Cell Mean is computed as:
And a T or with a period in the subscript means to collapse over that factor (with the position of the subscript
telling which factor to collapse). Thus, in the table above, the A marginals are shown in burgandy and the B marginals
are shown blue.
Note that the grand N=npq. Also note that since the calculations become much more difficult with unequal ns, we
will only cover the situation of equal ns.
III. Logic
The logic of the two way ANOVA is a direct extension of the one variable case. For the one variable case, we
partitioned the total variability into two pieces. In terms of the Sum of Squares:
In the two way ANOVA, there will be a source of variance for each effect as well as the error term. In terms of the Sum
of Squares:
Thus, there are five deviations involved:
For SSA, we are interested in the deviations of the A marginals about the grand mean. In symbols:
For the actual formula, we need to square and sum these deviations over all subjects.
For SSB, we are interested in the deviations of the B marginals about the grand mean. In symbols:
For SSwithin, we are interested in the deviations of the individual scores from their cell means. In symbols:
For SSAxB, we are interested in the deviations of the cell means from the grand mean minus the effects of
factors A and B. In symbols:
This reduces to:
or, more simply:
For SST, we are interested in the deviations of the individual scores from the grand mean. In symbols:
And for the degrees of freedom, we have:
dfA =p-1
dfB =q-1
dfAxB =(p-1)(q-1)
=pq-p-q+1
dfwithin =pq(n-1)
=pqn-pq
=N-pq
dfT =npq-1
=N-1
IV. Formal Example

1. Research Question
There are several (corresponding to the effects in the analysis):
Does prenatal alcohol effect PA learning in rats?
Does PA learning change with age?
Do the effects of prenatal alcohol depend on the age of testing?
2. Hypotheses
Since there are several research questions, we need a pair of hypotheses for each question. One problem is that we
are going to have complications in terminology (i.e., too many µs). So let's use Greek letters. For example, let α =
the main effect of A and β = the main effect of B. More specifically:
Says α1 equals the mean for the population for all groups in the first level of factor A minus the mean of the total
population of scores. If there is no effect, this should be equal to zero.
Note also that:
Thus:
Factor A:
In Symbols In Words
HO Prenatal alcohol has no effect on PA.
HA Not Ho Prenatal alcohol does have an effect on PA.
Factor B:
In Symbols In Words
HO Age is unrelated to PA learning.
HA Not Ho Age is related to PA learning.
A x B Interaction:
In Symbols In Words
HO The effect of alcohol

does not depend on age.
HA Not Ho The effect of alcohol

does depend on age
3. Assumptions
1. The null hypothesis.
2. The groups are sampled randomly.
3. The population distribution of the DV is normal in shape.
4. The groups are independent. (Note that the factorial design can handle dependent conditions, but it is
beyond the scope of this course.)
5. The population variances are homogenous.
6. n's are equal and greater than 1 (typically at least 5).
7. Factors are fixed, that is, the experimenter purposely chose the levels of the IVs. (Given the introductory
nature of the course and the fact that this is the most common scenario encountered, this issue will not be
discussed further.)
4. Decision rules
We are going to work with a 2x2 factorial design with 5 subjects per group. Thus:
dfA =p-1 =2-1 =1

dfB =q-1 =2-1 =1
dfAxB =(p-1)(q-1) =(2-1)(2-1) =1
=pq-p-q+1
dfwithin =pq(n-1) =2*2(5-1) =16
=pqn-pq
=N-pq
dfT =npq-1 =(5*2*2)-1 =19
=N-1
Notice that the df add up to the total. This info allows us to create a grid showing the critical values for the
F ratio (obtained from the F table):
Source A B AxB
df 1/16 1/16 1/16
Fcrit 4.49 4.49 4.49
The 2x2 case is simple, that is, all three critical values are the same. If Fobs ≥ Fcrit, reject Ho. Otherwise do
not reject Ho.
5. Computation - [Minitab]
Here is the data (i.e., the number of trials to learn PA):
Young Older
Age ->
b1 b2
0% 35% 0% 35%
Maternal Diet -> a1 a2 a1 a2
5 18 6 6
4 19 7 9
Data 3 14 5 5
4 12 8 9
2 15 4 3
18 78 30 32
n=njk 5 5 5 5
3.6 15.6 6 6.4
The relevant descriptive statistic is the means, and, in the case of an ANOVA, it is probably best to plot them:
Let's expand on the data grid for the calculations.
Age -> b1 b2
Maternal Diet -> a1 a2 a1 a2
X X2 X X2 X X2 X X2
5 25 18 324 6 36 6 36
4 16 19 361 7 49 9 81
Data
3 9 14 196 5 25 5 25
4 16 12 144 8 64 9 81
2 4 15 225 4 16 3 9
18 78 30 32 158 T
n=njk 5 5 5 5 20 N
3.6 15.6 6 6.4
70 1250 190 232 1742 II
The following "totals table" helps with computing marginal totals.
b1 b2
a1 18 30 48
Tj.s
a2 78 32 110
96 62 158
T.ks T..
Now we will need five quantities. Note, in the interest of saving some space, all intermediate quantities
are not shown. All steps are shown in the practice problems.
I.
II.
III.
IV.
V.
And now we can compute the SS's:
SSA= III-I= 1440.4-1248.2= 192.2

SSB= IV-I= 1306.0-1248.2= 57.8
SSAxB= V+I-III-IV= 1666.4+1248.2-1440.4-1306.0= 168.2
SSW= II-V= 1742.0-1666.4= 75.6
SST= II-I= 1742.0-1248.2= 493.8
We check that the Sum of Squares add up to the total and they do. Thus, remembering that:
and
We can fill in the ANOVA summary table:
Source SS df MS F p
A 192.2 1 192.2 40.68 ≤.05
B 57.8 1 57.8 12.23 ≤.05
AxB 168.2 1 168.2 35.60 ≤.05
Within 75.6 16 4.725
Total 493.8 19
6. Decision
Since we have three research questions, we also have three decisions to make. Since all three Fobs values are
greater than the Fcrit (i.e., 4.49), we reject Ho in each case.
1. There is a main effect of prenatal alcohol which says that animals receiving alcohol in utero showed
impaired passive avoidance learning when compared to controls.
2. There is a main effect of age which says that mature animals learned the task more quickly.
3. There is an interaction which says that prenatal alcohol produces a deficit in the ability to withhold
responding which dissipates as the animal matures.
Note that given this pattern of data (which are fictitious but based upon fact), we would not pay attention to the
main effects. The main effect of age is not true for the 0%EDC animals. The main effect of alcohol is not true for
the adult animals. Thus, the interaction is what is worth paying attention to in this study.
V. Comparisons Revisited
In the example we have given of the 2x2 ANOVA, the outcome is clear. However, what if we had employed a 3x3
factorial design? That is, we include another control group that receives a normal, Lab Chow (LC) diet and we test the
animals at either 30, 80, or 130 days of age. There are two types of analysis that should be mentioned here. I should note
that in an effort to keep things simple, I will not ask you to actually perform these analyses. However, they follow
logically from what we have been doing and it is certainly worth your while to be aware of their existence.
1. Further Analysis of Main Effects
If there was no interaction and a significant main effect, we could do an analysis similar to what we did when
using the protected t test with the one way ANOVA. Below is a formula to determine the Least Significant
Difference (LSD) between means that is worthy of our attention. The procedure is essentially the same as for the
protected t, however, in this case, the main effect is reflected in the marginal means which changes the formula
slightly, and we are computing an LSD rather than an F ratio which also shifts things around a bit.
Consider the hypothetical example below:
In this case, the analysis would reveal that the significant main effect of maternal diet is due to the fact that the
animals receiving alcohol in utero took longer to learn PA that did controls (which did not differ among
themselves).
2. Simple Main Effects of the Interaction
If, however, the interaction was significant, we might want to look at the simple main effects of the interaction.
This analysis looks at the difference between the cell means for one factor at each of the levels of the other. The
least significant difference between the means is computed with a slight modification to the formula we used
above, that is:
The hypothetical data presented below (which, in this case, is based on the actual data obtained in the experiment)
shows a significant interaction.
Computing the simple main effects of the interaction would show that the animals receiving alcohol in utero took
significantly longer to learn PA at 30 days of age. At 80 days, the effect was marginal and at 130 days there was
no effect. Furthermore, the analysis would show that the two control groups were not significantly different at any
age.
Copyright © 1997-2012 M. Plonsky, Ph.D.

Comments? mplonsky@uwsp.edu.

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Psych. Statistics: Two way analysis of variance (ANOVA).

Analysis of Variance - Two Way

Practice Problems (Answers)

the design. Note that EDC refers to Ethanol Derived Calories.

Factor A - addresses whether maternal diet effects PA learning.

More generally, we speak of several kinds of effects:

Treatment Effect - a difference in population means. There are two kinds:

2. The Notion of an Interaction

3. Main effect of factor B

(factor A) (35% EDC) 4 4 4

Maternal Diet (0% EDC) 3 1 2

Maternal Diet (0% EDC) 2 4 3

Maternal Diet (0% EDC) 3 3 3

Maternal Diet (0% EDC) 1 1 1

3. Advantages of the Factorial Design

There are three important advantages to the factorial design:

Two Group Design Factorial Design

2. Experimental Control & Increased Generality of the Results

a2 Xi21 Xi22 Xi2k Xi2q

Xn21 Xn22 Xn2k Xn2q

aj Xij1 Xij2 Xijk Xijq

ap Xip1 Xip2 Xipk Xipq

Thus, there are five deviations involved:

This reduces to:

or, more simply:

And for the degrees of freedom, we have:

IV. Formal Example

Note also that:

HO Prenatal alcohol has no effect on PA.

HA Not Ho Prenatal alcohol does have an effect on PA.

HO Age is unrelated to PA learning.

HA Not Ho Age is related to PA learning.

HO The effect of alcohol

HA Not Ho The effect of alcohol

dfA =p-1 =2-1 =1

Here is the data (i.e., the number of trials to learn PA):

3.6 15.6 6 6.4

Let's expand on the data grid for the calculations.

3.6 15.6 6 6.4

70 1250 190 232 1742 II

The following "totals table" helps with computing marginal totals.

And now we can compute the SS's:

SSA= III-I= 1440.4-1248.2= 192.2

We can fill in the ANOVA summary table:

responding which dissipates as the animal matures.

1. Further Analysis of Main Effects

Consider the hypothetical example below:

2. Simple Main Effects of the Interaction

Copyright © 1997-2012 M. Plonsky, Ph.D.

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