T Test

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T Test

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COMPSTAT Group

www.compstatgroup.com

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Key Concepts

t Test

Chi-square Test

Cochran-Mantel-Haenszel Test

Contents

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Null Hypothesis

There is no (statistically) significant difference between male and female

students with respect to their math achievement

Alternative Hypothesis

There is a (statistically) significant difference between male and female

students with respect to their math achievement

Type I error

Reject the null hypothesis when it is true. Probability of type I error is

denoted by

Type II error

Fail to reject the null hypothesis when it is false. Probability of type II

error is denoted by

Hypothesis Testing

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Power of the test

To be able to reject the null hypothesis when it is true, denoted by 1-

Variation

Chance variation

Effect variation

The difference that we might find between the boys, and girls' exam

achievement in our sample might have occurred by chance, or it might exist in

the population

P Value

Probability of getting a result as extreme as or more extreme than the one observed

when the null hypothesis is true .

When our study results in a probability of 0.01We say that the likelihood of getting the

difference we found by chance would be 1 in a 100.

The smaller the P value the greater the evidence we have against the null hypothesis.

What we usually do is compare the p-value with some pre-specified (a-priori) value

which we call a (the significance level). If p is less than a, we reject the null hypothesis

and accept the alternative hypothesis.

Hypothesis Testing

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Steps in testing of hypothesis

State null hypothesis and the alternative hypothesis

Select the level of significance

Select a sample and calculate its mean

Calculate the test statistic

Compare the calculated test statistic with tabulated

If calculated value > tabulated value

then reject the Null Hypothesis at that level of significance and for

that degrees of freedom. Otherwise do not reject it.

We can also compute the corresponding p-values -

If p-value < (level of significance) then reject Ho

Hypothesis Testing

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Let xi (i=1,2,3.n) be a random sample of size n

from a normal population with mean and variance

2

then students t is defined by the statistic

with (n-1) d. f.

where x is sample mean and S

2

is unbiased estimate

of the population variance.

t Test

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assumptions

The parent population from which the sample is

drawn is normal

T he sample observations are independent i.e. the

sample is random

The population standard deviation is unknown

t Test

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Types of t Test

One sample t Test

t Test for two independent (uncorrelated) samples

Equal variance

Unequal variance

t Test for paired (correlated) samples

t Test

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One Sample t test

Compare the mean of a single group of

observation with a specified (hypothetical) value.

Assumptions:

Subjects are randomly drawn from a population and the

distribution of the mean being tested is normal.

Standard deviation is unknown.

t Test

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How to test

Let Xi (i=1, 2n) be a sample of size n from a population with specified

mean.

H

o

: There is no significant difference between sample mean and

population mean.

H

1

: Sample mean is not equal to population mean (Two tailed test)

Or

H

1

: Sample mean >Population mean (Right tailed test)

Or

H

1

: Sample mean < Population mean. (Left tailed test)

t Test

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Example: One sample t test

data time;

input time @@;

datalines;

43 90 84 87 116 95 86 99 93 92

121 71 66 98 79 102 60 112 105 98

;

run;

proc ttest h0=80 alpha=0.1;

var time;

run;

The VAR statement indicates that the time variable is being studied, while

the H0= option specifies that the mean of the time variable should be

compared to the value 80 rather than the default null hypothesis of 0.

This ALPHA= option requests 10% confidence intervals rather than the

default 5% confidence intervals.

t Test

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Test Statistic

Then compare this calculated value with the tabulated value.

If t (calculated) > t (tabulated ) then reject H

o

If t (calculated) < t (tabulated) then accept H

o

Example:

Comparison of mean dietary intake of a particular group of individuals

with the recommended daily diet.

t Test

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t Test

Output

Summary statistics appear at the top of the output. The sample size (N), the mean and its

confidence bounds (Lower CL Mean and Upper CL Mean), the standard deviation and its

confidence bounds (Lower CL Std Dev and Upper CL Std Dev), and the standard error are

displayed with the minimum and maximum values of the time variable. The test statistic, the

degrees of freedom, and the p-value for the t test are displayed next; at the 10% -level, this

test indicates that the mean length of the court cases are significantly different from 80 days

(t=2.30, p=0.0329).

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Comparison of two independent means

A t test is used when we wish to compare two means

Assumptions

The samples are random and independent of each other.

Parent population from which samples are coming is normally distributed.

The variances are equal in both the groups if variances are not equal , modified

t test is used.

Normality of data is tested by using normality test such as Shapiro-Wilk

test and Kolmogorov Smirnov test.

Equality of variance is tested either by F test ,Levenes test or Bartletts

test.

t Test

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Type of data required

Independent variable one nominal variable with two

levels e.g. Boy/girl student, non smoking /heavy smoking

mothers

Dependent variable Continuous variable e.g. Marks

obtained by the students in annual exam , birth weight of

baby

t Test

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How to test

Let X

i

(i=1, 2n

1

) and Y

j

(j=1, 2n

2

) be two samples of size n

1

and n

2

H

o

: There is no significant difference in means of two groups

H

1

: There is significant difference in means of two groups (Two tailed

test)

Or

H

1

: mean of first group > mean of second group (Right tailed test)

Or

H

1

: mean of first group < mean of second group (Left tailed test)

t Test

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t Test

Test Statistic

With equal variance

Where S

p

is pooled variance of two groups

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t Test

With unequal variance

Then compare this calculated value with the tabulated value.

If t (calculated) > t (tabulated ) then reject Ho

If t (calculated) < t (tabulated) then accept Ho

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In SAS PROC TTEST is used to calculate the t statistic for two independent

sample.

In SAS output

If Prob F > 0.05 consider Prob T corresponding to Equal Variances.

If Prob F <=0.05 consider Prob T corresponding to Unequal Variances.

The test statistic is a students t-test with N-2 degrees of freedom, where N

is the total number of subjects.

A low p-value indicates evidence to reject the null hypothesis in favor of the

alternative. In other words, there is evidence that the means are not equal.

t Test

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The syntax for the TTEST procedure is

PROC TTEST <options>;

CLASS variable; <statements>;

The CLASS statement specifies the grouping variable for the analysis.

The data for this grouping variable must contain two and only two

values.

Example:

PROC TTEST;

CLASS GROUP;

VAR SCORE;

RUN;

t Test

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Example

Data Hospital;

input gender days;

lines;

1 13

1 15

1 9

1 18

1 11

1 20

1 24

1 22

1 25

2 11

2 14

2 10

2 8

2 16

2 9

2 17

2 21

RUN;

proc format;

value gender 1='male'

2='female';

run;

proc ttest;

class gender;

var days;

title 'two sample t-test for the difference

between the two population means';

run;

t Test

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Output 1

Output 2

Output3

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Paired t test

Used to compare means on the same or related subject over time or

in differing circumstances; subjects are often tested in a before-

after situation .

Same individuals are studied more than once in different

circumstances.

e.g. Measurements made on the same people before and after

intervention

The outcome variable should be continuous.

The difference between pre - post measurements should be

normally distributed.

t Test

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Test Statistic

Suppose we want to test the efficacy of a particular drug for inducing sleep.

Let Xi and Yi (i=1,2n) be the reading in hours of sleep on the ith individual before and

after the drug is given respectively.

H

o

: There is no effect of drug on sleeping hours

H

1

: The new drug increases the sleeping hours.

calculate the test statistics t and

If t (calculated) > t (tabulated )

Then reject Ho and conclude that the new drug increases sleeping hours.

t Test

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If t (calculated) > t (tabulated)

Then accept Ho and conclude that there is no effect of the drug

on the sleeping hours.

Note: We can also compute the corresponding p-values and can

conclude in following manner

If p-value > 0.05 then accept Ho and conclude that there is no

effect of the new drug on sleeping hours.

If p-value < 0.05 then reject Ho and conclude that the new drug

increases the sleeping hours.

t Test

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If one wants to do paired t test with PROC MEANS in SAS, create a new

variable (say diff) in the DATA step, subtracting one tested variable from

the other.

Example

PROC MEANS;

BY GROUP;

VAR DIFF;

RUN;

If one wants to do paired t test with PROC TTEST in SAS, use paired

statement . The CLASS and VAR statements cannot be used with the

PAIRED statement.

Example

PROC TTEST';

PAIRED BEFORE *AFTER;

RUN;

t Test

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Example:

Data sleeping_pill;

input subject pill placebo;

lines;

1 7.3 6.8

2 8.5 7.9

3 6.4 6.0

4 9.0 8.4

5 6.9 6.5

RUN;

Using Paired option of proc t test:

proc ttest;

paired pill*placebo;

title 'paired t-test for the difference between the two population means';

run;

t Test

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Getting p value by calculating difference

data compare;

set sleeping_pill;

difference=pill-placebo;

run;

proc ttest data=compare;

var difference;

title 'An alternative paired t-test: t-test on the differences';

Using proc univariate

proc univariate data=compare;

var difference;

title 'Univariate test to get signed rank test and sign test';

run;

t Test

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Output 1:

Paired t-test for the difference between the two

population means

The TTEST Procedure

Output 2:

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t Test

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Syntax :

PROC TTEST < options > ;

CLASS variable ;

PAIREDvariables ;

BY variables ;

VAR variables ;

FREQ variable ;

WEIGHT variable ;

t Test

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PROC TTEST < options > ;

The following options can appear in the PROC TTEST statement.

ALPHA=p

specifies that confidence intervals are to be 100(1-p)% confidence intervals, where 0<p<1.

By default, PROC TTEST uses ALPHA=0.05. If p is 0 or less, or 1 or more, an error

message is printed.

CI=EQUAL

CI=UMPU

CI=NONE

specifies whether a confidence interval is displayed for and, if so, what kind. The

CI=EQUAL option specifies an equal tailed confidence interval, and it is the default. The

CI=UMPU option specifies an interval based on the uniformly most powerful unbiased

test of . The CI=NONE option requests that no confidence interval be displayed for . The

values EQUAL and UMPU together request that both types of confidence intervals be

displayed. If the value NONE is specified with one or both of the values EQUAL and

UMPU, NONE takes precedence.

COCHRAN

requests the Cochran and Cox (1950) approximation of the probability level of the

approximate t statistic for the unequal variances situation.

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DATA=SAS-data-set

names the SAS data set for the procedure to use. By default, PROC TTEST uses the most

recently created SAS data set. The input data set can contain summary statistics of the

observations instead of the observations themselves. The number, mean, and standard

deviation of the observations are required for each BY group (one sample and paired

differences) or for each class within each BY group (two samples).

H0=m requests tests against m instead of 0 in all three situations (one-sample, two-sample,

and paired observation t tests). By default, PROC TTEST uses H0=0.

CLASS variable - A CLASS statement giving the name of the classification (or grouping)

variable must accompany the PROC TTEST statement in the two independent sample cases.

It should be omitted for the one sample or paired comparison situations. If it is used without

the VAR statement, all numeric variables in the input data set (except those appearing in the

CLASS, BY, FREQ, or WEIGHT statement) are included in the analysis. The class variable

must have two, and only two, levels. PROC TTEST divides the observations into the two

groups for the t test using the levels of this variable. You can use either a numeric or a

character variable in the CLASS statement.

BY variables -You can specify a BY statement with PROC TTEST to obtain separate analyses

on observations in groups defined by the BY variables. When a BY statement appears, the

procedure expects the input data set to be sorted in order of the BY variables.

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FREQ variable -The variable in the FREQ statement identifies a variable that contains the

frequency of occurrence of each observation. PROC TTEST treats each observation as if it

appears n times, where n is the value of the FREQ variable for the observation. If the value is

not an integer, only the integer portion is used. If the frequency value is less than 1 or is missing,

the observation is not used in the analysis. When the FREQ statement is not specified, each

observation is assigned a frequency of 1. The FREQ statement cannot be used if the DATA=

data set contains statistics instead of the original observations.

PAIRED PairLists -The PairLists in the PAIRED statement identifies the variables to be compared in

paired comparisons. You can use one or more PairLists. Variables or lists of variables are

separated by an asterisk (*) or a colon (:). The asterisk requests comparisons between each

variable on the left with each variable on the right. The colon requests comparisons between the

first variable on the left and the first on the right, the second on the left and the second on the

right, and so forth. The number of variables on the left must equal the number on the right when

the colon is used. The differences are calculated by taking the variable on the left minus the

variable on the right for both the asterisk and colon. A pair formed by a variable with itself is

ignored. Use the PAIRED statement only for paired comparisons. The CLASS and VAR

statements cannot be used with the PAIRED statement.

Examples of the use of the asterisk and the colon are shown in the following table.

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t Test

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VAR variables

-The VAR statement names the variables to be used in the

analyses. One-sample comparisons are conducted when the VAR

statement is used without the CLASS statement, while group

comparisons are conducted when the VAR statement is used with a

CLASS statement. If the VAR statement is omitted, all numeric variables

in the input data set (except a numeric variable appearing in the BY,

CLASS, FREQ, or WEIGHT statement) are included in the analysis. The

VAR statement can be used with one- and two-sample t tests and cannot

be used with the PAIRED statement.

WEIGHT variable -

The WEIGHT statement weights each observation in

the input data set by the value of the WEIGHT variable. The values of the

WEIGHT variable can be non-integral, and they are not truncated.

Observations with negative, zero, or missing values for the WEIGHT

variable are not used in the analyses. Each observation is assigned a

weight of 1 when the WEIGHT statement is not used. The WEIGHT

statement cannot be used with an input data set of summary statistics.

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CHI-SQUARE TEST

Chi-square test is used to test the

independence of two variables.

The chi-square test assumes that the

frequency for each cell is five or higher for

2 X 2 contingency table.

However, if this assumption is not met

then we have to go for Fisher's exact test.

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Chi-square Test

Expected= (row total * column total)/N;

Tabulated results of the Observed and Expected frequency

237 154 83 Total

(77.97) (42.03) 120 83 37 Girls

(76.02) (40.97) 117 71 46 Boys

Not in

trouble

(Expected)

Got into

trouble

(Expected)

Total Not in

trouble

(Observed)

Got into

trouble

(Observed)

237 154 83 Total

(77.97) (42.03) 120 83 37 Girls

(76.02) (40.97) 117 71 46 Boys

Not in

trouble

(Expected)

Got into

trouble

(Expected)

Total Not in

trouble

(Observed)

Got into

trouble

(Observed)

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Expected values are the results we would

expect if the null hypothesis were true.

we calculate the difference between the

observed (O) and expected (E) frequency in

each cell, square that difference, and then

divide that by the Expected value.

chi-square= sum ((O - E)

2

/E)

Degrees of freedom= (r-1)(c-1)

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What is the difference between a Chi-square test and Fishers exact

test?

Both test the association between two categorical variables.

The difference is that the Chi-square test requires the

expected cell counts in the crosstabulation of these two

categorical variables to be larger than 5. When this

assumption fails Fisher's exact test is recommended.

We can use Fisher's Exact Test when one of the cells in the

table has a zero in it.

Fisher's Exact Test is also very useful for highly

imbalanced tables. If one or two of the cells in a two by two

table have numbers in the thousands and one or two of the

other cells has numbers less than 5, we can still use

Fisher's Exact Test.

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Fisher's Exact Test can be calculated with PROC FREQ by

specifying the Exact option in the TABLES statement.

How do you interpret the p-value of a Chi-square test or

Fishers exact test?

We begin by assuming there is no association between the

two (categorical) variables. In technical terms this is called

the null hypothesis. The alternative hypothesis would state

the two variables are associated is some way.

The p-value of a Chi-square test or Fishers exact test tells

us the likelihood of getting more extreme results than what

we got. If our assumption is correct then a p-value of 0.01

would suggest the chance of getting more extreme results

than we currently got is very small. In this case we have

evidence to suggest our assumption of no association is not

correct. Hence it would be reasonable to claim there is an

association between the two variables.

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WHEN & WHY

The Cochran-Mantel-Haenszel (CMH) test compares two groups

on a binary response (yes, no ), adjusting for control variables.

The initial data are represented as a series of K 2x2 contingency

tables, where K is the number of strata. Traditionally, in each

table the rows correspond to the "Treatment group" values (e.g

"Placebo", "Drug A") and the column to the "Response" values (e.g

"No change," "Improvement").

The null hypothesis is that the response is conditionally

independent of the treatment in any given strata.

The stratification of the subjects into K groups (according to the

values of controlled variables - e.g. "Age group") increases the

power of the test to detect association. This increase in power

comes from comparing like subjects to like subjects

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Layout

Assume there are k strata (k>=2). Within

Stratum j, there are N

j

patients (j= 1, 2,...,

k), randomly allocated to one of the two

groups. In group 1, there are n

j1

patients,

X

j1

of whom are considered responders.

Similarly, group 2 has n

j2

patients with

X

j2

responders.

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Cochran-Mantel-Haenszel Test

Assume there are k strata (k>=2). Within Stratum j, there are N

j

patients (j= 1, 2,..., k), randomly

allocated to one of the two groups. In group 1, there are n

j1

patients, X

j1

of whom are

considered responders. Similarly, group 2 has n

j2

patients with X

j2

responders.

Layout

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Let p

1

and p

2

denote the overall response rates for Group1 and

Group2 respectively for stratum j ,compute the quantities

num

j

=(X

j1

.n

j2

-X

j2

.n

j1

)/N

j

and

den

j

=n

j1

.n

j2

.(X

j1

+X

j2

).(N

j

-X

j1

-X

j2

)/N

j2

.(N

j

-1)and calculate the

Test Statistic =(num

j

)2/ den

j

Compare the calculated value of test statistic with tabulate and

accordingly reject or do not reject the null hypothesis.

In SAS CMH can be calculated with PROC FREQ by specifying

the CMH option in the TABLES statement.

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Example : Computing Cochran-Mantel-Haenszel Statistics for a Stratified

Table

The data set Migraine contains hypothetical data for a clinical

trial of migraine treatment. Subjects of both genders receive

either a new drug therapy or a placebo. Their response to

treatment is coded as 'Better' or 'Same'. The data are recorded as

cell counts, and the number of subjects for each treatment and

response combination is recorded in the variable Count.

data Migraine;

input Gender $ Treatment $ Response $ Count @@;

datalines;

female Active Better 16 female Active Same 11 female Placebo

Better 5 female Placebo Same 20 male Active Better 12

male Active Same 16 male Placebo Better 7 male Placebo

Same 19 ;

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The following statements create a three-way table

stratified by Gender, where Treatment forms the rows and

Response forms the columns. The CMH option produces the

Cochran-Mantel-Haenszel statistics. For this stratified 22

table, estimates of the common relative risk and the

Breslow-Day test for homogeneity of the odds ratios are

also displayed. The NOPRINT option suppresses the

display of the contingency tables. These statements

produce output 1 through output3.

proc freq data=Migraine;

weight Count;

tables Gender*Treatment*Response / cmh noprint;

title1 'Clinical Trial for Treatment of Migraine Headaches';

run;

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For a stratified 22 table, the three CMH

statistics displayed in output1 test the

same hypothesis.

The significant p-value (0.004) indicates

that the association between treatment

and response remains strong after

adjusting for gender.

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The large p-value for the Breslow-Day test

(0.2218) in output3

indicates no significant gender difference

in the odds ratios.

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THANKS

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