BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.
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Transcript of BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.
![Page 1: BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649e695503460f94b65674/html5/thumbnails/1.jpg)
BIOL 4605/7220
Ch 13.3 Paired t-test
GPT LecturesCailin XuOctober 26,
2011
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Overview of GLM
GLM
Regression
ANOVA
ANCOVA
One-Way ANOVA
Two-Way ANOVA
Simple regression Multiple
regression
Two categories (t-test)
Multiple categories - Fixed (e.g., treatment, age)
- Random (e.g., subjects, litters)
2 fixed factors 1 fixed & 1 random
(e.g., Paired t-test)
Multi-Way ANOVA
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GLM: Paired t-test
Two factors (2 explanatory variables on a nominal
scale)
One fixed (2 categories)
The other random (many categories)
+Fixed factor
Random factor
Remove var. among units → sensitive test
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GLM: Paired t-test
Effects of two drugs (A & B) on 10 patients
Fixed factor: drugs (2 categories: A & B)
Random factor: patients (10)
Remove individual variation (more sensitive test)
An Example:
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GLM: Paired t-test
Hours of extra sleep (reported as averages) with
two
Drugs (A & B), each administered to 10 subjects
Response variable: T = hours of extra sleep
Explanatory variables: drug & subject
Data:
Fixed Nominal scale (A &
B)
Random Nominal scale (0, 1, 2, . . .
, 9)
)( DX )( SX
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
ANOVA
Recompute p-value?
Declare decision: AHvsH .0Report & Interpr.of
parameters
Yes
No
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General Linear Model (GLM) --- Generic
Recipe Construct model
Verbal model
Hours of extra sleep (T) depends on drug ( ) DX
Graphical model (Lecture notes Ch13.3, Pg 2)
Formal model (dependent vs. explanatory variables)
GLM form:
Exp. Design Notation:
resXXXXT SDSDSSDD 0
ijkijjiijk BBT )(
Fixed
Random
Interactive
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General Linear Model (GLM) --- Generic
Recipe Construct model
Formal model
GLM form: resXXXXT SDSDSSDD 0
Fixed
Random
Interactive effect
GLM form: resXXT SSDD 0
- Appears little/no- Limited data- Assume no
Fixed
Random Break
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Place data in an appropriate format
Execute analysis in a statistical pkg: Minitab, R
Minitab:
MTB> GLM ‘T’ = ‘XD’ ‘XS’;
SUBC> fits c4;
SUBC> resi c5.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ANOVA table, fitted values, residuals | (more commands to obtain parameter estimates)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Place data in an appropriate format
Execute analysis in a statistical pkg: Minitab, R
Minitab:
MTB> means ‘T’
MTB> ANOVA ‘T’ = ‘XD’ ‘XS’;
SUBC> means ‘XD’ ‘XS’.
hours54.1ˆ0
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XD N MeansDrug effect
(fixed)
-1 10 0.75 -0.79
1 10 2.33 0.79
XS N MeansSubject effect
(random)
0 2 1.3 -0.24
1 2 -0.4 -1.94
2 2 0.45 -1.09
3 2 -0.55 -2.09
4 2 -0.1 -1.64
5 2 3.9 2.36
6 2 4.6 3.06
7 2 1.2 -0.34
8 2 2.3 0.76
9 2 2.7 1.16
Output from Minitab
hoursD 79.0ˆ
Means minus grand mean = parameter
estimates for subjects
0̂
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Place data in an appropriate format
Execute analysis in a statistical pkg: Minitab, R
Minitab:
R: library(lme4)
model <- lmer(T ~ XD + (1|XS), data = dat) fixef(model)
fitted(model) residuals(model)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
-- No line fitted, so skip
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
Homogeneous residuals?
-- res vs. fitted plot (Ch 13.3, pg 4: Fig.1)
-- Acceptable (~ uniform) band; no
cone
(skip)
(√)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
Homogeneous residuals?
If n small, assumptions met?
(skip)
(√)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
Homogeneous residuals?
If n (=20 < 30) small, assumptions
met?
1) residuals homogeneous?
2) sum(residuals) = 0? (yes, least squares)
(skip)
(√)
(√)
(√)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
Homogeneous residuals?
If n (=20 < 30) small, assumptions
met?
1) residuals homogeneous?
2) sum(residuals) = 0? (least squares)
3) residuals independent?
(Pg 4-Fig.2; pattern of neg. correlation, because
every value within A, a value of opposite sign within
B)
(Pg 4-Fig.3; res vs. neighbours plot; no trends up or
down within each drug)
(skip)
(√)
(√)
(√)
(√)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
(Residuals)
Straight line assumption
Homogeneous residuals?
If n small, assumptions met?
1) residuals homogeneous?
2) sum(residuals) = 0? (least squares)
3) residuals independent?
4) residuals normal?
- Residuals vs. normal scores plot (straight
line?)
(Pg 4-Fig. 4) (YES, deviation small)
(skip)
(√)
(√)
(√)
(√)
(√)
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
All measurements of hours of extra
sleep, given the mode of collection
1). Same two drugs
2). Subjects randomly sampled with
similar characteristics as in the sample
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing?
Research question: Do drugs differ in effect, controlling for
individual variation in response to the drugs?
Hypothesis testing is appropriate
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
Hypothesis for the drug term: (not interested in whether subjects differ)
)()(:
)()(:
0 BDAD
BDADA
TMeanTMeanH
TMeanTMeanH
0:
0:
0
D
DA
H
H
Yes
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
Hypothesis for the drug term: (not interested in whether subjects differ)
Test statistic: F-ratio Distribution of test statistic: F-distribution Tolerance of Type I error: 5% (conventional level)
Yes
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
ANOVA
Yes
![Page 24: BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649e695503460f94b65674/html5/thumbnails/24.jpg)
General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource
XXTGLM SSDD
:
: 0
ANOVA
df : (20-1) = ? + ? + ? = (2-1) + (10-1) + (19-1-9) = 1 + 9 + 9
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General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
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General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
![Page 27: BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649e695503460f94b65674/html5/thumbnails/27.jpg)
General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
}]ˆ)([]ˆ)({[10 20
20 BDAD TmeanTmean
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General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
210
10ˆ2/2
iBDAD TT
![Page 29: BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649e695503460f94b65674/html5/thumbnails/29.jpg)
General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
SDTol SSSSSS
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General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
756.0/48.12/ resD MSMS
![Page 31: BIOL 4605/7220 Ch 13.3 Paired t-test GPT Lectures Cailin Xu October 26, 2011.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649e695503460f94b65674/html5/thumbnails/31.jpg)
General Linear Model (GLM) --- Generic
Recipe
Calculate & partition df according to model
resSubjectDrugTotalSource :
ANOVA Table
ANOVA
df : 19 = 1 + 9 + 9
Source df SS MS F p
Drug 1 12.48 12.48 16.5 0.0028
Subject 9 58.08 6.45
Res 9 6.81 0.756
Total 19 77.37
MTB > cdf 16.5;SUBC> F 1 9. R:x P( X <= x ) 1-pf(16.5,1,9) 16.5 0.997167
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
ANOVA
Recompute p-value?
Yes
Deviation from normal
small
p-value far from 5%
No need to recompute
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
ANOVA
Recompute p-value?
Declare decision: AHvsH .0
Yes
.:
.:0drugsondependssleepextraHaccept
drugsondependnotsleepextraHreject
A
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General Linear Model (GLM) --- Generic
Recipe Construct model
Execute model
Evaluate model
State population; is sample representative?
Hypothesis testing? State pairAHH /0
ANOVA
Recompute p-value?
Declare decision: AHvsH .0Report & Interpret
parameters
Yes
No
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General Linear Model (GLM) --- Generic
Recipe Report parameters & confidence
limits Subject: random factor, means of no
interest Drug effects ( )
hoursTmean
hoursTmean
BD
AD
33.2)(
75.0)(
S.E. Lower limit Upper limit
0.5657 -0.53 hours 2.03 hours
0.6332 0.90 hours 3.76 hours
262.2]9[025.0 t
C.L. overlap, because subject variation is not controlled statistically
)10/()( BorADTsd
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Paired t-test --- Alternative way
Calculate the difference within each random category
t-statistic
)(0028.0);(0014.0
)9(06.4:
0
58.1
)(
0
tailstwotailonep
dfstatistict
hours
TTmeanT ADBDdiff
S.E. L U
0.389 0.70 hours 2.46
hours
1,
/
220
n
ress
ns
Tt diff
diff
diff
Strictly positive, significant difference between the drugs
Current example
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Subject Drug A Drug B
1 0.7 1.9
2 -1.6 0.8
3 -0.2 1.1
4 -1.2 0.1
5 -0.1 -0.1
6 3.4 4.4
7 3.7 5.5
8 0.8 1.6
9 0 4.6
10 2 3.4
Data (hours of extra sleep)
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Graphical model
A B-2
-1
0
1
2
3
4
5
6
Drug
Ho
urs
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Data format in Minitab & R
T XD XS0.7 -1 0-1.6 -1 1-0.2 -1 2-1.2 -1 3-0.1 -1 43.4 -1 53.7 -1 60.8 -1 70 -1 82 -1 9
1.9 1 00.8 1 11.1 1 20.1 1 3-0.1 1 44.4 1 55.5 1 61.6 1 74.6 1 83.4 1 9
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SubjectDrug ADrug
B Diff Fits Res
1 0.7 1.9 1.2 1.58 -0.38
2 -1.6 0.8 2.4 1.58 0.82
3 -0.2 1.1 1.3 1.58 -0.28
4 -1.2 0.1 1.3 1.58 -0.28
5 -0.1 -0.1 0.0 1.58 -1.58
6 3.4 4.4 1.0 1.58 -0.58
7 3.7 5.5 1.8 1.58 0.22
8 0.8 1.6 0.8 1.58 -0.78
9 0 4.6 4.6 1.58 3.02
10 2 3.4 1.4 1.58 -0.18
Data (hours of extra sleep)