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morning session

1

Statistics Micro Mini

Multi-factor ANOVA

January 5-9, 2008

Beth Ayers

January 7, 2009 -

morning session

2

Thursday Sessions

ANOVA

One-way ANOVA

Two-way ANOVA

ANCOVA

With-in subject

Between subject

Repeated measures

MANOVA

etc.

January 7, 2009 -

morning session

3

What is ANOVA?

ANalysis Of VAriance

Partitions the observed variance based on

explanatory variables

Compare partitions to test significance of

explanatory variables

January 7, 2009 -

morning session

4

Some Terminology

Between subjects design each subject

participates in one and only one group

Within subjects design the same group of

subjects serves in more than one treatment

Subject is now a factor

Mixed design a study which has both between

and within subject factors

Repeated measures general term for any study

in which multiple measurements are measured

on the same subject

Can be either multiple treatments or several

measurements over time

January 7, 2009 -

morning session

5

ANOVA

Use variances and variance like

quantities to study the equality or non-

equality of population means

So, although it is analysis of variance we

are actually analyzing means, not

variances

There are other methods which analyze

the variances between groups

January 7, 2009 -

morning session

6

ANOVA

Typical exploratory analysis includes

Tabulation of the number of subjects in each

experimental group

Side-by-side box plots

Statistics about each group

At least mean and standard deviation, can

include 5-number summary and information on

skewness

Table of means for each experimental group

January 7, 2009 -

morning session

7

Notation

If we have k groups, denote the means

of the groups as:

1

,

2

, . . .,

k

Student i in group j has observation

y

ij

=

j

+

ij

Where

ij

are independent, distributed N(0,

2

)

Can combine this and say subjects from

group j have distribution N(

j

,

2

)

With random assignment, the sample

mean for any treatment group is

representative of the population mean

for that group

January 7, 2009 -

morning session

8

Assumptions

1. The errors

ij

are normally distributed

2. Across the conditions, the errors have

equal spread. Often referred to as

equal variances.

Rule of thumb: the assumption is met if the

largest variance is less than twice the

smallest variance

If unequal variances need to make a

correction!! This is usually /2.

3. The errors are independent from each

other

January 7, 2009 -

morning session

9

Checking the assumptions

Use the residuals, which are the

estimates of

ij

1. Look at normal probability plot

2. Look at residual versus fitted plot

3. Hard to check, often assumed from study

design

For mild violations of the assumptions,

there are options for correction

When the assumptions are not

met the p-value is simply

wrong!!

January 7, 2009 -

morning session

10

One-way ANOVA

One-way ANOVA is used when

Only testing the affect of one explanatory

variable

Each subject has only one treatment or

condition

Thus a between-subjects design

Used to test for differences among two

or more independent groups

Gives the same results as two-sample T-

test if explanatory variable has 2 levels

January 7, 2009 -

morning session

11

Hypothesis Testing

H

0

:

1

=

2

= . . . =

k

H

1

: the s are not all equal

The alternative hypothesis H

1

:

1

k

is wrong!

The null hypothesis is called the overall null and is

the hypothesis tested by ANOVA

If the overall null is rejected, must do more specific

hypothesis testing to determine which means are

different, often referred to as contrasts

January 7, 2009 -

morning session

12

Terminology

The sample variance is the sum of the squared

deviations from the mean divided by the degrees of

freedom

A mean square (MS) is a variance like quantity

calculated as a SS/df

df

SS

MS

1

) (

s

2

2

N

x x

i

January 7, 2009 -

morning session

13

One-way ANOVA

In one-way ANOVA we work with two mean

square quantities

MS

within

the mean square within-groups

MS

between

the mean square between-groups

between

between

between

df

SS

MS

within

within

within

df

SS

MS

January 7, 2009 -

morning session

14

Within vs. Between

January 7, 2009 -

morning session

15

One-way ANOVA

For each individual group we have

So the estimate of MS

within

is

And the estimate of MS

between

is

1

) (

df

SS

MS

1

2

between

between

between

k

x x n

k

i

i i

k

i

i

k

i

i

k N n

SS

1

1

within

within

within

) 1 (

df

SS

MS

1

) (

df

SS

1

2

i

i

i

n

j

i ij

n

x x

i

January 7, 2009 -

morning session

16

Mean Squares

What do these values mean?

MS

within

is considered a true estimate of

2

that is

unaffected by whether the null or alternative

hypothesis is true

MS

between

is considered a good estimate of

2

only

when the null hypothesis is true

If the alternative is true, values of MS

between

tend to be

inflated

Thus, we can look at the ratio of the two mean

square values to evaluate the null hypothesis

January 7, 2009 -

morning session

17

Testing the Hypothesis

The F-test looks at the variation among the group

means relative to the variation within the sample

The F-statistic tends to be larger if the alternative

hypothesis is true than if the null hypothesis is true

The test statistic F has an F(k-1, N-k) distribution

) (

) 1 (

k N

SS

k

SS

df

SS

df

SS

MS

MS

F

within

between

within

within

between

between

within

between

January 7, 2009 -

morning session

18

What does the F ratio tell us?

F = MS

between

/ MS

within

The denominator is always an estimate of

2

(under both the null and alternative hypotheses)

The numerator is either another estimate of

2

(under the null) or is inflated (under the

alternative)

If the null is true, values of F are close to 1

If the alternative is true, values of F are larger

Large values of F depend on the degrees of

freedom

January 7, 2009 -

morning session

19

The ANOVA table

When running an ANOVA, statistical packages will

return an ANOVA table summarizing the SS, MS, df,

F-statistic, and p-value

SS Df MS F Sig

Group

(Treatment,

between)

SS

between

df

between

MS

between

MS

between

_________________

MS

within

P-value

Residual

(Error,

within)

SS

within

df

within

MS

within

Total SS

between

+ SS

within

df

between

+ df

within

January 7, 2009 -

morning session

20

Example

Suppose we want to know if typing

speed varies across majors

Use 4 majors Biology, Business,

English, and Mathematics

H

0

: typing speed is the same for

students of all majors

H

0

:

Bio

=

Business

=

Eng

=

Math

H

1

: typing speed varies across the

majors

H

1

: at least one of the means is different

January 7, 2009 -

morning session

21

Box plots

January 7, 2009 -

morning session

22

Summary

Major n

i

Mean Variance

Biology 25 45.3 24.7

Business 25 47.6 25.4

English 25 55.6 38.8

Mathematics 25 45.1 20.1

The largest variance is less than twice the smallest

variance (38.8 < 2 20.1 = 40.2). Use = 0.05.

January 7, 2009 -

morning session

23

Degrees of Freedom

How many groups do we have?

What is the sample size?

Using these values:

What is df

within

?

What is df

between

?

January 7, 2009 -

morning session

24

Degrees of Freedom

How many groups do we have?

There are k = 4 groups Biology, English,

Business, and Mathematics

What is the sample size?

There are N = 100 students

Using these values,

What is df

between

?

k 1 = 4 1 = 3

What is df

within

?

N k = 100 4 = 96

January 7, 2009 -

morning session

25

Sample Output

SS Df MS F Sig

Group

(Treatment,

between)

1807.49 3 602.50 22.091 0.000

Residual

(Error,

within)

2618.20 96 27.17

Total 4425.69 99

Our estimate of

2

is 27.17

The numerator MS = 602.5 and appears

to be highly inflated

January 7, 2009 -

morning session

26

Results

F-statistic = 22.1

P-value: <0.0005

Conclusion the average words per

minute differs for at least one of the

majors

To make stronger statements need to do

further testing

January 7, 2009 -

morning session

27

Checking the assumptions

January 7, 2009 -

morning session

28

Further Analysis

If H

0

is rejected, we conclude that not all

the s are equal

Would like to make statements about

where there are differences

Can use planned or unplanned

comparisons (or contrasts)

Planned comparisons are interesting

comparisons decided on before analysis

Unplanned comparisons occur after seeing the

results

Be careful not to go fishing for results

January 7, 2009 -

morning session

29

Contrasts

A simple contrast hypothesis compares

two population means

H

O

:

1

=

5

A complex contrast hypothesis has

multiple population means on either side

H

0

: (

1

+

2

) / 2 =

3

H

0

: (

1

+

2

) / 2 = (

3

+

4

+

5

) / 3

January 7, 2009 -

morning session

30

Planned Comparisons

Most statistical packages allow you to

enter custom planned contrast

hypotheses

The p-values are only valid under strict

conditions

The conditions maintain Type-1 error rate

across the whole experiment

Computer packages assume that you

have checked the assumptions of the

ANOVA test

January 7, 2009 -

morning session

31

Conditions for Planned

Comparisons

Contrasts are selected before looking at the

residuals, they are planned not post-hoc

Must be ignored if the overall null is not rejected!

Each contrast is based on independent

information from other contrasts

The number of planned comparisons must not be

more than the corresponding degrees of freedom

(k-1 in one-way ANOVA)

January 7, 2009 -

morning session

32

Unplanned Comparisons

What if we notice a possible interesting

difference when looking at the results?

Can do comparisons but need to adjust

the -level to control for Type-1 error

One common method is to use Tukeys

simultaneous confidence intervals to

calculate any and all pairs of group

population means

This procedure takes multiple comparisons

into consideration to preserve the level

January 7, 2009 -

morning session

33

Other Options

Bonferroni correction for the number of

comparisons done

Dunnetts tests

Scheffe procedure

January 7, 2009 -

morning session

34

Tukeys Multiple Comparisons for

previous example

January 7, 2009 -

morning session

35

Conclusions

In the table on the previous page,

1 = Biology, 2 = Business, 3 = English,

4 = Mathematics

Biology, Business, and Mathematics are

all are significantly different from English

There are no other significant

differences

January 7, 2009 -

morning session

36

Additional sample output

Below is the same output from a

different software package

January 7, 2009 -

morning session

37

Comparison to Regression

Sample regression output

Which major is our baseline?

January 7, 2009 -

morning session

38

Comparison to Regression

F-statistic = 22.1, p-value < 0.0005

This is the same F-statistic and p-value as the

ANOVA on slide 25

At least one of the explanatory variables

is important in this corresponds to the

rejection of the null, at least one of the

means differs

January 7, 2009 -

morning session

39

Comparison to Regression

Note that Biology is the baseline and 45.3 is the

mean WPM for Biology students

Note that Business and Mathematics are not

significant

Agrees with post-hoc comparisons that neither

Business or Mathematics is significantly different

from Biology, but English is not

To make further conclusions will need to look at

multiple comparisons, such as the previous

Tukey intervals

January 7, 2009 -

morning session

40

Regression

The conclusions about the overall null

hypothesis will be the same

In regression can make statements

comparing groups to baseline

To make more conclusive statements

will need to do more analysis

ANOVA and either planned or post-hoc

comparisons will do the same thing and

is often easier

January 7, 2009 -

morning session

41

One-way ANOVA Power

Two different SAT prep courses charge

$1200 for a two month course. An

(unethical) experiment would be to

randomize students into one of the two

courses or take no course

What information is needed to calculate

power for this one-way ANOVA?

Sample size

Within group variance (

2

)

Estimated or minimally interesting outcome

means for each group

January 7, 2009 -

morning session

42

Estimate of

2

Based on previous years, we know that

95% of the student scores on SATs fall

between 900 and 1500

= (1500-900)/4 = 150

2

= 150^2

January 7, 2009 -

morning session

43

Minimally interesting outcome

What is the minimally average benefit,

in points gained, that would justify the

program?

The minimally interesting outcome is based

on previous knowledge

For this example well try several

different values

January 7, 2009 -

morning session

44

sd[treatment]

Different applets will define things slightly

different. Find an applet you understand.

For the applet I will show you, they require

sd[treatment]. From their definition this is

calculated as

Where

i

is the i

th

group mean

k = the number of groups

Ready to go to power applet

1 - k

) (

nt] sd[treatme

k

1 i

2

i

January 7, 2009 -

morning session

45

Calculating the power

Let = 150, n = 50, effect = 50 points

Power = 0.3811

Let = 150, n = 100, effect = 50 points

Power = 0.6772

Let = 150, n = 50, effect = 100 points

Power = 0.9367

Let = 150, n = 50, effect = 25 points

Power = 0.1245

January 7, 2009 -

morning session

46

Calculating the power

Let = 100, n = 50, effect = 50 points

Power = 0.7276

Let = 100, n = 100, effect = 50 points

Power = 0.9622

Let = 100, n = 50, effect = 100 points

Power = 0.997

Let = 100, n = 50, effect = 25 points

Power = 0.2294

January 7, 2009 -

morning session

47

Moving past One-way ANOVA

What if we have two categorical explanatory

variables?

What if we have categorical and quantitative

explanatory variables?

What if subjects have more than one treatment?

What if there is more than one response

variable?

And many other combinations

January 7, 2009 -

morning session

48

Two-way ANOVA

Suppose we now have two categorical

explanatory variables

Is there a significant X

1

effect?

Is there a significant X

2

effect?

Are there significant interaction effects?

If X

1

has k levels and X

2

has m levels,

then the analysis is often referred to as

a k by m ANOVA or k x m ANOVA

January 7, 2009 -

morning session

49

Terminology

If the interaction is significant, the

model is called an interaction model

If the interaction is not significant, the

model is called an additive model

Explanatory variables are often referred

to as factors

January 7, 2009 -

morning session

50

Assumptions

The assumptions are the same as in

One-way ANOVA

1. The errors

ij

are normally distributed

2. Across the conditions, the errors have equal

spread. Often referred to as equal variances.

3. The errors are independent from each other

January 7, 2009 -

morning session

51

Two-way ANOVA

Two-way (or multi-way) ANOVA is an

appropriate analysis method for a study

with a quantitative outcome and two (or

more) categorical explanatory variables.

The assumptions are Normality, equal

variance, and independent errors.

January 7, 2009 -

morning session

52

Results

Results are again displayed in a ANOVA

table

Will have one line for each term in the

model. For a model with two factors, we

will have one line for each factor and

one line for the interaction. We will also

have a line for the error and the total.

See next page.

January 7, 2009 -

morning session

53

The ANOVA table

SS df MS F Sig

Factor 1 k-1

Factor 2 m-1

Interaction (k-1)(m-1)

Error N-k*m *

Total N-1

The MS(error), denoted by * in the above table, is

the true estimate of

2

The MS in each row is that rows SS/df

The F-statistic is the MS/MS(error)

January 7, 2009 -

morning session

54

Exploratory Analysis

Table of means

Interaction or profile plots

An interaction plot is a way to look at

outcome means for two factors

simultaneously

A plot with parallel lines suggests an additive

model

A plot with non-parallel lines suggests an

interaction model

Note that an interaction plot should NOT be

the deciding factor in whether or not to run

an interaction model

January 7, 2009 -

morning session

55

Example

Continuing with the previous example,

suppose wed like to add gender as an

explanatory variable

X

1

: Major 4 levels

X

2

: Gender 2 levels

Response: words per minute typed

We will fit an 4 by 2 ANOVA

January 7, 2009 -

morning session

56

Table of Means and Counts

Male Female Overall

Biology 45.5 45.2 45.4

Business 48.6 46.9 47.6

English 55.3 55.9 55.6

Mathematics 45.6 44.6 45.1

Overall 48.9 47.9 48.4

Male Female

Biology 14 11

Business 10 15

English 14 11

Mathematics 12 13

Note, this

table should

also include

the standard

error of each

of the means.

January 7, 2009 -

morning session

57

Interaction plots

January 7, 2009 -

morning session

58

Interaction plots

There are two ways to do an interaction plot.

Both are legitimate. Ease of interpretation is the

final criteria of which to do.

If one explanatory variable has more levels than

the other, interpretation is often easier if the

explanatory variable with more levels defines the

x-axis

If one explanatory variable is quantitative but

has been categorized and the other is

categorical, interpretation is often easier if the

categorized quantitative variable defines the x-

axis.

Example: age, 20-29, 30-39, 40-49, etc.

January 7, 2009 -

morning session

59

Results

Typical output:

The last column contains the p-

values

Always check interaction first!

If the interaction is not significant, rerun

without it

January 7, 2009 -

morning session

60

Results

Updated results

Now we can interpret the main effects. We can

see that major is significant but that gender is

not.

January 7, 2009 -

morning session

61

Checking the assumptions

January 7, 2009 -

morning session

62

Notes

If the interaction is significant, do not

check the main effects. The main

effects should always be kept if the

interaction is significant.

Note that due to the groups of students,

you will see vertical lines in the residual

versus predicted plot. This is due to the

fact that all students with a particular

combination of the factors will have the

same predicted value.

January 7, 2009 -

morning session

63

Example 2

Using the same variables, lets look at a

different outcome

January 7, 2009 -

morning session

64

Table of Means Example 2

Male Female Overall

Biology 37.9 45.8 41.2

Business 39.9 45.0 43.0

English 45.3 60.0 51.8

Mathematics 41.8 50.0 46.1

Overall 41.3 49.8 51.2

January 7, 2009 -

morning session

65

Typical SPSS Exploratory Analysis

January 7, 2009 -

morning session

66

Interaction plots Example 2

January 7, 2009 -

morning session

67

Results Example 2

Results

Note that the interaction is significant

In this case both main effects are also

significant, however since the interaction is

significant we would keep them even if they

were not

January 7, 2009 -

morning session

68

Example 2

January 7, 2009 -

morning session

69

Example 2

January 7, 2009 -

morning session

70

Example 3

Again, using the same variables, lets

look at a different outcome

January 7, 2009 -

morning session

71

Table of Means Example 3

Male Female Overall

Biology 47.9 47.2 47.6

Business 50.2 48.1 49.0

English 54.8 62.1 58.1

Mathematics 52.0 48.4 50.1

Overall 51.3 51.1 58.0

January 7, 2009 -

morning session

72

Interaction Plots Example 3

January 7, 2009 -

morning session

73

Results Example 3

Results

In this case, the interaction and major

are significant, but gender is not.

Since the interaction is significant, leave

gender in the model.

January 7, 2009 -

morning session

74

Example 3

January 7, 2009 -

morning session

75

Example Ginkgo for Memory

A study was performed to test the

memory effects of the herbal medicine

Ginkgo biloba in healthy people.

Subjects received a daily dosage

(placebo, 120mg, 250mg) for two

months. Subjects also received one of

two types of mnemonic training. All

subjects were given a memory test

before the study and again at the end.

The response variable is the difference

(after before) in memory test scores.

There were 18 subjects randomly

assigned to each combination of levels.

January 7, 2009 -

morning session

76

Exploratory Analysis

January 7, 2009 -

morning session

77

Exploratory Analysis

January 7, 2009 -

morning session

78

SPSS ANOVA output

Conclusions?

January 7, 2009 -

morning session

79

ANOVA output

Conclusions?

January 7, 2009 -

morning session

80

Estimated Profile Plot

January 7, 2009 -

morning session

81

Post-hoc Comparisons

Since there are only two levels of

training and there is a significant

training effect, we dont need multiple

comparisons for training

January 7, 2009 -

morning session

82

Residual plot

No problems

January 7, 2009 -

morning session

83

Further Analysis

If there had been an interaction, we

could create a table indicating which

differences were significant

January 7, 2009 -

morning session

84

ANCOVA

Analysis of Covariance

At least one quantitative and one categorical

explanatory variable

In general, the main interest is the effects of

the categorical variable and the quantitative

variable is considered to be a control variable

It is a blending of regression and ANOVA

January 7, 2009 -

morning session

85

Example

Suppose that we have two different

math tutors and would like to compare

performance on the final math test

We also have time on tutor and would

like to use that as another explanatory

variable

January 7, 2009 -

morning session

86

Exploratory Analysis

January 7, 2009 -

morning session

87

Compare Regression and ANCOVA

Regression

ANCOVA

January 7, 2009 -

morning session

88

Compare Regression and ANOVA

Note that the p-value for the interaction

is the same in both models

The interaction is not significant, drop

and rerun

89

Compare Regression and ANOVA

Regression

ANCOVA

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