ANalysis Of VAriance

Contents
• Introduction – Various statistical tests
• What is ANOVA?
• One way ANOVA
• Two way ANOVA
• MANOVA (Multivariate ANalysis Of VAriance)
• ANOVA with repeated measures
• Other related tests
• References
 Summary Table of Statistical Tests
Sample Characteristics
Level of
2 Sample K Sample (i.e., >2) Correlation
Measurement
1 Sample
Independent Dependent Independent Dependent

Categorical or Χ2 or Χ2 Macnarmar’s Χ2 Cochran’s Q

Nominal bi- Χ2
nomina
l

Rank or Mann Wilcoxin Kruskal Friedman’s Spearman’s

Ordinal Χ2 Whitney U Matched rho
Pairs Signed Wallis H ANOVA
Ranks

Parametric z test t test t test 1 way ANOVA 1 way ANOVA

(Interval & or between within between (within or Pearson’s
t test groups groups repeated r
Ratio) groups measure)

Factorial (2 way) ANOVA

 What is ANOVA

 Statistical technique specially designed to

test whether the means of more than 2
quantitative populations are equal.

 Developed by Sir Ronald A. Fisher in

1920’s.
EXAMPLE: Study conducted among men of age group
18-25 year in community to assess effect of Socio
Economic Status on BMI

Lower SES Middle SES Higher SES

18,17,18,19,19 22,25,24,26,24,21 25,26,24,28,29
N1= 5 N2= 6 N3= 5
Mean=18.2 Mean= 23.6 Mean=26.4
 ANOVA

One way ANOVA Two way ANOVA Three way ANOVA

Effect of SES on BMI Effect of age & SES on BMI Effect of age, SES, Diet
on BMI

ANOVA with repeated measures - comparing >=3 group means

where the participants are same in each group. E.g.
Group of subjects is measured more than twice, generally over
time, such as patients weighed at baseline and every month after
a weight loss program
One Way ANOVA
 Data required
One way ANOVA or single factor ANOVA:
• Determines means of
≥ 3 independent groups
significantly different from one another.

• Only 1 independent variable (factor/grouping variable)

with ≥3 levels
• Grouping variable- nominal
• Outcome variable- interval or ratio
Post hoc tests help determine where difference exist
 Assumptions
1) Normality: The values in each group are
normally distributed.
2) Homogeneity of variances: The variance within
each group should be equal for all groups.
3) Independence of error: The error(variation of
each value around its own group mean) should
Skewness
be independent for each value.
Kurtosis
Kolmogorov-Smirnov
Shapiro-Wilk test
Box-and-whiskers plots
Histogram
 Steps
1. State null & alternative hypotheses

2. State Alpha
3. Calculate degrees of Freedom
4. State decision rule

5. Calculate test statistic

- Calculate variance between samples
- Calculate variance within the samples
- Calculate F statistic
- If F is significant, perform post hoc test

6. State Results & conclusion

1. State null & alternative hypotheses

H0  1  2...  i
H0 : all sample means are equal

Ha  not all of the i are equal

At least one sample has different mean
2. State Alpha i.e 0.05

3. Calculate degrees of Freedom

K-1 & n-1
k= No of Samples,
n= Total No of observations

4. State decision rule

If calculated value of F >table value of F, reject Ho

5. Calculate test statistic

Calculating variance between samples

1. Calculate the mean of each sample.

2. Calculate the Grand average
3. Take the difference between means of various
samples & grand average.
4. Square these deviations & obtain total which
will give sum of squares between samples (SSC)
5. Divide the total obtained in step 4 by the
degrees of freedom to calculate the mean sum
of square between samples (MSC).
Calculating Variance within Samples

1. Calculate mean value of each sample

2. Take the deviations of the various items in a
sample from the mean values of the respective
samples.
3. Square these deviations & obtain total which
gives the sum of square within the samples (SSE)
4. Divide the total obtained in 3rd step by the
degrees of freedom to calculate the mean sum
of squares within samples (MSE).
 The mean sum of squares

Calculation of MSE
Calculation of MSC- Mean Sum Of
Mean sum of Squares Squares within
between samples
samples

SSC SSE
MSC  MSE 
k 1 nk
k= No of Samples, n= Total No of observations
 Calculation of F statistic
Variabilit y between groups
F
Variabilit y within groups

𝑀𝑆𝐶
F- statistic =
𝑀𝑆𝐸

Compare the F-statistic value with F(critical) value which is

obtained by looking for it in F distribution tables against
degrees of freedom. The calculated value of F > table value
H0 is rejected
 Between-group variance is large relative to the
within-group variance, so F statistic will be
larger & > critical value, therefore statistically
significant .
Between-Group
Variance Conclusion – At least one of group means is
Within-Group
significantly different from other group means
Variance
 Within-group variance is larger, and the
between-group variance smaller, so F will
Between-Group be smaller (reflecting the likely-hood of
Variance
no significant differences between these
Within-Group
Variance
3 sample means)
 Post-hoc Tests
• Used to determine which mean or group of means is/are
significantly different from the others (significant F)
• Depending upon research design & research question:
 Bonferroni (more powerful)
Only some pairs of sample means are to be tested
Desired alpha level is divided by no. of comparisons

 Tukey’s HSD Procedure

when all pairs of sample means are to be tested

 Scheffe’s Procedure (when sample sizes are unequal)

 One way ANOVA: Table
Source of SS (Sum of Degrees of MS (Mean Variance
Variation Squares) Freedom Square) Ratio of F

Between SSC k-1 MSC= MSC/MSE

Samples SSC/(k-1)

Within SSE n-k MSE=

Samples SSE/(n-k)

Total SS(Total) n-1

 Example- one way ANOVA
Example: 3 samples obtained from normal
populations with equal variances. Test the
hypothesis that sample means are equal

8 7 12
10 5 9
7 10 13
14 9 12
11 9 14
1.Null hypothesis –
No significant difference in the means of 3 samples

2. State Alpha i.e 0.05

3. Calculate degrees of Freedom

k-1 & n-k = 2 & 12

4. State decision rule

Table value of F at 5% level of significance for d.f 2 & 12 is 3.88
The calculated value of F > 3.88 ,H0 will be rejected

5. Calculate test statistic

 X1 X2 X3
8 7 12
10 5 9
7 10 13
14 9 12
11 9 14
Total 50 40 60
M1= 10 M2 = 8 M3 = 12

Grand average = 10+ 8 + 12

= 10
3
Variance BETWEEN samples (M1=10, M2=8,M3=12)

Sum of squares between samples (SSC) =

n1 (M1 – Grand avg)2 + n2 (M2– Grand avg)2 + n3(M3– Grand avg)2
5 ( 10 - 10) 2 + 5 ( 8 - 10) 2 + 5 ( 12 - 10) 2 = 40

Calculation of Mean sum of Squares between samples (MSC)

SSC 40
MSC    20
k 1 2

k= No of Samples, n= Total No of observations

Variance WITH IN samples (M1=10, M2=8,M3=12)
X1 (X1 – M1)2 X2 (X2– M2)2 X3 (X3– M3)2

8 4 7 1 12 0
10 0 5 9 9 9
7 9 10 4 13 1
14 16 9 1 12 0
11 1 9 1 14 4
30 16 14
Sum of squares within samples (SSE) = 30 + 16 +14 = 60
Calculation of Mean Sum Of Squares within samples (MSE)

SSE 60
MSE    5
n  k 12
 Calculation of ratio F

Variabilit y between groups

F
Variabilit y within groups

𝑀𝑆𝐶
F- statistic = = 20/5 =4
𝑀𝑆𝐸

The Table value of F at 5% level of significance for d.f 2 & 12 is 3.88

The calculated value of F > table value
H0 is rejected. Hence there is significant difference in sample means
Short cut method -
X1 (X1) 2 X2 (X2 )2 X3 (X3 )2

8 64 7 49 12 144
10 100 5 25 9 81
7 49 10 100 13 169
14 196 9 81 12 144
11 121 9 81 14 196
Total 50 530 40 336 60 734

Total sum of all observations = 50 + 40 + 60 = 150

Correction factor = T2 / N=(150)2 /15= 22500/15=1500
Total sum of squares= 530+ 336+ 734 – 1500= 100
Sum of square b/w samples=(50)2/5 + (40)2 /5 + (60) 2 /5 - 1500=40
Sum of squares within samples= 100-40= 60
 Example with SPSS
Example:
Do people with private health insurance visit their
Physicians more frequently than people with no
insurance or other types of insurance ?
N=86
• Type of insurance - 1.No insurance
2.Private insurance
3. TRICARE
• No. of visits to their Physicians(dependent variable)
 Violations of Assumptions
Normality
Choose the non-parametric Kruskal-Wallis H Test
which does not require the assumption of
normality.
Homogeneity of variances
 Welch test or
 Brown and Forsythe test or Kruskal-Wallis H Test
Two Way ANOVA
 Data required
• When 2 independent variables
(Nominal/categorical) have
an effect on one dependent variable
(ordinal or ratio measurement scale)

• Compares relative influences on Dependent Variable

• Examine interactions between independent variables
• Just as we had Sums of Squares and Mean Squares in One-
way ANOVA, we have the same in Two-way ANOVA.
 Two way ANOVA
Include tests of three null hypotheses:
1) Means of observations grouped by one factor are
same;

2) Means of observations grouped by the other factor

are the same; and

3) There is no interaction between the two factors.

The interaction test tells whether the effects of one
factor depend on the other factor
Example-
we have test score of boys & girls in age group
of 10 yr,11yr & 12 yr. If we want to study the
effect of gender & age on score.

Two independent factors- Gender, Age

Dependent factor - Test score
Ho -Gender will have no significant effect on student
score
Ha -

Ho - Age will have no significant effect on student

score
Ha -

Ho – Gender & age interaction will have no

significant effect on student score
Ha -
 Two-way ANOVA Table

Source of Degrees of Sum of Mean P-value

Variation Freedom Squares Square F-ratio

Factor A r1 SSA MSA FA = MSA / MSE Tail area

Factor B c 1 SSB MSB FB = MSB / MSE Tail area

Interaction (r – 1) (c – 1) SSAB MSAB FAB = MSAB / MSE Tail area

Error rc(n – 1) SSE MSE

(within)
Total rcn  1 SST
 Example with SPSS
Example:
Do people with private health insurance visit their
Physicians more frequently than people with no
insurance or other types of insurance ?
N=86 Gender
0-M
• Type of insurance - 1.No insurance
1-F
2.Private insurance
3. TRICARE
• No. of visits to their Physicians(dependent variable)
 MANOVA
Multivariate ANalysis Of VAriance
 Data Required

• MANOVA is used to test the significance of the

effects of one or more Independent variables on
two or more Dependent Variabless.

• It can be viewed as an extension of ANOVA

with the key difference that we are dealing with
many dependent variables (not a single DV as
in the case of ANOVA)
• Dependent Variables ( at least 2)
– Interval /or ratio measurement scale
– May be correlated
– Multivariate normality
– Homogeneity of variance

• Independent Variables ( at least 1)

– Nominal measurement scale
– Each independent variable should be independent of
each other
• Combination of dependent variables is called
“joint distribution”

• MANOVA gives answer to question

“ Is joint distribution of 2 or more DVs significantly
related to one or more factors?”
• The result of a MANOVA simply tells us that a
difference exists (or not) across groups.
• It does not tell us which treatment(s) differ or
what is contributing to the differences.
• For such information, we need to run ANOVAs
with post hoc tests.
Various tests used-
 Wilk's Lambda
 Widely used; good balance between power and
assumptions
 Pillai's Trace
 Useful when sample sizes are small, cell sizes are unequal,
or covariances are not homogeneous
 Hotelling's (Lawley-Hotelling) Trace
 Useful when examining differences between two groups
 Example with SPSS
Example:
Do people with private health insurance visit their
Physicians more frequently than people with no
insurance or other types of insurance ?
N=50 Gender(0-M,1-F)
• Type of insurance - 1.No insurance
Satisfaction with
2.Private insurance facility provided
3. TRICARE
• No. of visits to their Physicians(dependent variable)
Research question
1. Do men & women differ significantly from each
other in their satisfaction with health care provider &
no. of visits they made to a doctor

2. Do 3 insurance groups differ significantly from each

other in their satisfaction with health care provider &
no. of visits they made to a doctor

3. Is there any interaction b/w gender & insurance

status in relation to satisfaction with health care
provider & no. of visits they made to a doctor
ANOVA with repeated measures
 ANOVA with Repeated Measures

• Determines whether means of 3 or more

measures from same person or matched controls
are similar or different.

• Measures DV for various levels of one or more

IVs

• Used when we repeatedly measure

the same subjects multiple times
 Assumptions

• Dependent variable is interval /ratio (continuous)

• Dependent variable is approximately normally
distributed.
• One independent variable where participants are
tested on the same dependent variable at least 2
times.

• Sphericity- condition where variances of the differences

between all combinations of related groups (levels) are equal.
 Sphericity violation
• Sphericity can be like homogeneity of variances
in a between-subjects ANOVA.
• The violation of sphericity is serious for the
Repeated Measures ANOVA, with violation
causing the test to have an increase in the Type I
error rate).
• Mauchly's Test of Sphericity tests the assumption
of sphericity.
 Sphericity violation
• The corrections employed to combat violation of
the assumption of sphericity are:
 Lower-bound estimate,
 Greenhouse-Geisser correction and
 Huynh-Feldt correction.

• The corrections are applied to the degrees of

freedom (df) such that a valid critical F-value can
be obtained.
 Steps ANOVA
1.Define null & alternative hypotheses

2. State Alpha
3. Calculate degrees of Freedom
4. State decision rule

5. Calculate test statistic

- Calculate variance between samples
- Calculate variance within the samples
- Calculate ratio F
- If F is significant, perform post hoc test

6. State Results & conclusion

Calculate Degrees of Freedom for
• D.f between samples = K-1
• D.f within samples = n- k
• D.f subjects=r -1
• D.f error= d.f within- d.f subjects
• D.f total = n-1
State decision rule
If calculated value of F >table value of F, reject Ho
Calculate test statistic ( f= MS bw/ MS error)

SS DF MS F
Between
Within
-subjects
- error
Total

State Results & conclusion

 Example with SPSS
Example-
Researcher wants to observe the effect of
medication on free T 3 levels before, after 6 week,
after 12 week. Level of free T 3 obtained through
blood samples. Are there any differences between 3
conditions using alpha 0.05?
 Independent Variable- time 1, time 2, time 3
 Dependent Variable- Free T3 level
Other related tests-

ANCOVA (Analysis of Covariance)

Additional assumptions-
- Covariate should be continuous variable
- Covariate & dependent variable must show a
linear relationship & must be similar in each group
MANCOVA (Multivariate analysis of covariance)
One or more continuous covariates present
 References
• Methods in Biostatistics by BK Mahajan
• Statistical Methods by SP Gupta
• Basic & Clinical Biostatistics by Dawson and Beth
• Munro’s statistical methods for health care
research