Download as pdf or txt
Download as pdf or txt
You are on page 1of 97

Experimental Design and Statistical

Analysis of BioExperiments


:
.
. : :
- :
- H0=m1=m2=m3=M, :

.
- :
)Y=a+b(x

Y m T E
) Residual error( E,m. T .



.


:

.
:

.

.
Factors

Treatments:




.

:


Control :


Replication


. Fisher

.

.
.
.

.
.

.

. :
. :
.
. :
.
. :


. :

Coefficient of variation (C.V.) :


- = CV
.

CV -

.

CV
CV
CV
.


Experimental error


.
:
. )
...(
.

.


.
.
.

.
. .
.
Covariance
.


/


= F

MST
MSE


. = df
SS

.
- C.V


.
.
.

:
.
.
. ) (
.

.
.
.
.
.

(
. Formulation of the research plan

:



.

.

.






.




.
. Choice of factors to be used

:

(.
. Choice of variable to be
measured

:


.
) ( Dependent
variable


. .

: )
(

.
)
(
:

.
. Selction of experimental material
:
.
.
.
.
.
. Choice of experimental design

:
.

. )
...(.
. .
. .
.
.
. )(



.

.


.


/






. Formulation of amodel



. Collection of data




.
.
.
:



. Analysis of the data


.
.

.
:
SAS .
SPSS .
MINITAB .
. Conclusion and interpretations

:
.

.
.
.
.







...........
.
.
.

.
.


) paper (

.
.

.
.
.

.
.
.
.

Experimental error
,
:
. ) (.....
.
.
. )(



Replication

.
: )^ Min =( y-y Y
^ y .

Liner Model

) (
.
Yi= m+Ei

Yij= m+Ti+Eij

Fixed and random Effect

:


F
.

:




:
.

.

:
. Fixed effect model

. Random model

. Mixed effects model

The experimental program

population
:
. ) (
. . "
".
. .

. :Efficiency


. :

.
.

. .
. :
.
Unifactor experiment
Factorial experiments

.


) (
. )
(
Complete

) Randomized Block Desgin(RCPD



Incomplete Block Design

. .
.

) (
.









.

. ) (Variable
Y depended variable X

.
. )
(
.
.
)
.







.
.

.

.
.
.
.
.
.
.

SAS

.
.

Hypothsis testing


) (
:
. )Null Hypothesis (H0

.

. )Alternative Hypothesis (Ha


.

. :
. Type1 Error


. Type Error2

.

.

Significant level


) ( .
% %
%
.%


Primary experiments



.


.


:
.

.
) (

critical experiments


Observations

.
Experiment Extension



.

/
/


.
.

.
.


: Simple Experiments

...

.
: Factorial Experiments


.
:
.
.a
.b
.c
.d

. :
.a
.b


.
.

.
.
.

.

.
.


:
Quality Quantity

. Qualitative
.. :
- Nominal
: ....
- : Ordinal
.
. Quantitive
..... . :
- Intervel
- Ratis
:
) Continuous variables(
.
.

:

: t


) ( Discontinous variable Discrete


.
:
.
,
. .
:
.
.



:
.

Univariate anlalysis


. Bivariate analysis


:
. ) (
.
-: Dependent variable ) (
-:Independent variable ) (


independent

Dependent

Cluster analyst

Analysis of variance



. F

:
.
.
ANOVA Table

Pr> F

E.M.S

M.S

S.S

DF

F .

=m.s of T/m.s of E

S.O.V

=ss/df

:
- Additively Of The Main Effects
- Independence Of Errors

- Homogeneity Of Errors
- Normality Of Errors.

:
.
.
.

...

Proc GLM
GLM )
(

)) (Binomial

....


:
W: Shapiro-wilk normal test .
D: Kolomograv norm test
-

. Extremes

;Proc univariate normal plot

; Var Height weight


;Id subject

; Run


Proc sort By
.

.

Transformation of data




. :
 Log )Log(y+1

:

nonadditivity
=
.

) Log(y+1
.

 The Angular or Arcsine Transformation

) (
)

. (...

) % (%
.
:
-
%- .
 Square Root Transformation

) ( =
) Poisson (
+
, .

.
= ) (
) Binomial (
. (sin -1)Arcsin
.
%-
(-) %

N /
n/- n
SAS
. :
; Data ..
; Input ..X..Y
; Cards
..
; Proc Genmod
; Class
; Model Y=X/dist=poisson
; Dscale type3
; Run


.


SAS .

. Experimental design

. Treatment design
. ) (
)(
)(incomplate

. Response or sampling design )


( Sampling


:
:
.
.
.
:
:

. Lattice design


. Group balanced block design


Completely Randomized design
One way



.
:
.

.
.
.
.

.
.
:
.

.
.
:
.


) (
.
.
.
.
.
.
:


.
SAS

: :
.

. -
. - -
- .
. ) (

.


.

:
 .
 .
 .
 .

 .


)Randomized complete Block design (RCPD
Two Way

%

)
(

.
/



.
- .
-
- .

- .
-
-
-
-
-


).
(
:
-
-
- .
:
.

.
.

.
.
.
.
.
:
.


.
.
.
F
) ( )
(
:
.
.

. -

.

.
:






.

:
) (ABCDE


. :
.
. :
..... .
.
. : Panel Tests
.
. : .
. :
) ( .
. :

Latin square design


:
.


.
.
:
.

.
.

:
.


. -

.
-
.
-

-
)(
-

.
-

:
-
-
-
-

:
.
.

.
. ) ) ( (
LOG
. ) ( Variance data
...
+ -- =
=


Factor
. Level


.
,



Combinations
,

.


.
.
.
Exploration Exp,



.
.


Over a wide range of conditions

.


:
. Observation
) (
.
.

.
.

.

Incomplete Block

:

Interaction

. .
Response )
(.

:

.
) (
.
.
= .

Two Factor Experiments


)
(


.

:
.
.
.
. ) (
. ) (
.


) (

.

:
. .
. ) (

.

.
.
.

.


. Stabilty

.
. Distrbution sampling
Non Dis. Sampling
.Majerment over time
.

 

 "! 

 

  



2  /0 "%, )( %#


"%, 3 7) 8" # 8956 %#
<=9 %:;9

  

 

 


 
    NS    
   #" ! .
   * **       (  !
/      )*+ ,-   #

) (




Split plot design






Main plots

Subplots
Main

plot factor
. Sup plot factor
) ( .


.

.



) (
. : B
A
.

.
. : B

A B
A .


.
. :

) ( .

)
( .



.(...
(


.

.

.
.
.

.
.
.
.
.

:

A ) (
B .




.


.
)(
.
.


.
.

.
.

:
.
:
. .
. .
. .
. .
. .
. .
. .


r-1

Rep
Main plot
A
Error

a-1
)(r-1)(a-1

Sub Plot
B
A*B
Exp. Error

b-1
c-1
)(a-1)(b-1
)A(b-1)(r-1

; SAS Model =Rep A Rep*a B A*B


;Test h= Rep A e= Rep*a



    ) (

Strip Plot Design




,

.

.


.

)(

:
.

.
.

:
r-1

Rep

a-1

Horizontal factor A

)(r-1)(a-1

Error a

b-1

Vertical factor B

)(r-1)(b-1

Error b

)(a-1)(b-1

A*B

)(r-1)(a-1)(b-1

Exp. error

; SAS Model y = Rep A Rep*a B Rep*b A*B


; Test Rep A e= Rep*a
;e= Rep*b

Test h = B


Three or More Factor Experiments

...


- .



.


.
.

:
.
.
.


. ) ( split split plot

. ) ( strip split plot


Factorial in split split plot

)
(:

r-1
a-1
b-1
c-1
)(a-1)(b-1
)(a-1)(c-1
)(b-1)(c-1
)(a-1)(b-1)(c-1
)(r-1)(abc-1

Rep
Factor a
Factor b
Factor c
A*B
A*C
B*C
A*B*C
Exp. Error

;)SAS Model y = Rep A B C A*B A*C B*C A*B(C


Split Split Plot Design


 .




.


.. ) (

.
.

:
.
Main Plot
Sub plot Sub sub

Plot .
.
.

.


.
.

:
.
.

. Main plot

. Sub plot

. Factorial Experiment in

split plot
.

)(

.

Split plot in Factorial Experiment


.
.
.
) .... ( .

:
. )
(


r-1

Rep
Main plot
A
Error

a-1
)(r-1)(a-1

Sub plot
B
C
A*B
A*C
B*C
A*B*C
Exp. Error

b-1
c-1
)(a-1)(b-1
)(a-1)(c-1
)(b-1)(c-1
)(a-1)(b-1)(c-1
)(r-1)(abc-1

SAS Model = Rep A Rep*a B C A*B A*C B*C


;)A*B(C
;Test h= Rep A e= Rep*a

. )
(


r-1

Rep
Main plot
A
B
A*B
Error
Sub Plot
C
A*C
B*C
A*B*C
Exp. Error

a-1
b-1
)(a-1)(b-1
)(r-1)(ab-1
c-1
)(a-1)(c-1
)(b-1)(c-1
)(a-1)(b-1)(c-1
)A(bc-1)(r-1

SAS Model = Rep A Rep*a B C A*B A*C B*C


;(A*B(C
;Test h= Rep A e= Rep*a

.


). (

Rep

r-1

Main plot
A

a-1

)Error(a

)(r-1)(ab-1

Sub plot
B

b-1
)(a-1)(b-1

A*B

)a(b-1)(r-1

)Error(b
Sub Sub Plot
C

c-1
)(a-1)(c-1

A*C

)(b-1)(c-1

B*C
A*B*C

)(a-1)(b-1)(c-1

Exp. Error

)ab(c-1)(r-1

;)SAS Model =Rep A Rep*a B A*B Rep*a(b) C A*C B*C A*B(C


; Test h = Rep A e= Rep*a
;)Test h = B A*B e= Rep*a(b


Strip Split Plot Design


) (
.

:
 :
.
.
.
.
.

:
.

.

:
Rep

r-1

Horizontal factor A

a-1

Error a

(r-1)(a-1)

Vertical factor B

b-1

Error b

(r-1)(b-1)

A*B

(a-1)(b-1)

Error c

(r-1)(a-1)(b-1)

Sub Plot Factor C


A*C

(a-1)(c-1)

B*C

(b-1)(c-1)

A*B*C

(a-1)(b-1)(c-1)

Exp. error

(r-1) ab (c-1)

SAS Model y = Rep A Rep*a B Rep*b A*B Rep* A(B) C


A*C B*C A*B*C ;
Test Rep A

e= Rep*a ;

Test h = B

e= Rep*b;

Test h = A*B e= Rep*a(b)

Analysis of multi-observation


:
-
Non distractive

sampling
) (distractive sampling

.
-
.



.

plot sampling Measurement
over time

Plot Sampling



.


DF

S.O.V

t-1

Treatments

)T(r-1

Exp. error

)Rt(S-1

Sampling Error

SAS Model= tmt Sampling*tmt


Test H = tmt E= Sampling*Form

DF

S.O.V

r-1

Rep

t-1

Treatments

)T(r-1

Exp. error

)Rt(S-1

Sampling Error

SAS Model=Rep tmt Sampling rep* tmt

Test H =Rep tmt E= rep*tmt

Sampling Error
C.V MSE Sampling Error

CRD Sampling Error

Sampling Error



. Sampling Error
C.V. C.V. .

Nested Experiments





.



.


:
.

.

.
,
. ) (Formation

Measurement Over time



.

.
.

. )
....(
. )( RCBD

.
. ) (CRD


DF

S.O.V

t-1

Treatments

s-1

Sampling Or Time

)(t-1)(S-1

Sampling*tmt

)Rt(S-1

Exp. error

SAS Model= tmt Sampling*tmt



DF

S.O.V

r-1

Rep

t-1

Treatments

)(r-1)(t-1

Error a

s-1

Sampling Or Time

)(t-1)(S-1

Sampling*tmt

)T(r-1)(S-1

Exp. error

SAS Model=Rep tmt rep* tmt Sampling Sampling*tmt

Test H =Rep tmt E= rep*tmt



Spli Split plot





.


Analysis of Data Form a Series of Experiments

:
.
.
.





.

.


Comparisons Between Treatment Means





.
.
= )%(-

:

. )Least Significant Difference(LSD


Fisher LSD
.

LSD )

(
. LSD

) (.
.C.V


.
. )Duncan Multiple Range Test(DMRT
LSD
LSD LSD

.
.
. )Student Newman Koule Procedure( SNK

SNK
.
. Tukey's Method
LSD
Honest significant difference

)(

Lsd

F F
Duncan or S NK

SNK

Tukey,


.
. LSD
. LSD SNK
.
. Tukey's .
. SAS

:Contrast
LSD , NK ,

Duncan
.
:

)(

. =
. =

:
.
.
.
.
:
. )(
. .
. )(

.Contrast
Trt=4
Rep=3
Mse=0.116
Df=8
Y1=7.98
Y2=5.5
Y3=7.26
Y4=3.36


C=k1m1+ k2m2 +.Kt +Mt

K

Contrast 1= M1 (m2+m3+m4

SAS
Contrast ' title " Variable coefficient ;
Data ..;
Input .;
Cards;

Proc glm;
Clss variety;
Model y= variety/ss3;
Contrast 'variety verses variety ' variety 1 0 -1



.
......
.
.....
.

) Response (


.

) (
)
(
:





.



.
:




) (
). (
:

)
(


.

.
.
.
.
.

. Regression
Independent X
Dependent Y Y X X
Y
.

Correlation

.

:
.
.
.
.

: Regression
    Simple Linear Regression


.


Y
:
:
Y = a + bX

Y = a + b1X 1 + b 2 x 2

:
:Y )(.
:X .
: a,b .
a,b Y X .
:
: y :
.

x1 , x 2 ,..., x p

y = 0 + 1 x1 + 2 x 2 + .... + p x p +

0 , 1 ,..., p


:
. x1 , x2 ,..., x p .
. .
x
,
x
,...,
x
1
2
p

.
) ( 1 , 2 ,..., n

2 .I n

Simple Non Linear Regression



:
.


.

  ! " : Correlation


  6  2 5  2/ ' /0 ,)* , -. '  $!  )* r $
  8. / 1 ,

1 < r < 1 <2  ; , ' /0 , , -.? 2 >

D 6.B '!   6"F G 2E: 6.

 K '!  J2

M /0F J2 r > 0 , , -. ' 6E  

   , -.  *   -. O'<. 5

 /0F J2  r = 0 :  , , -.  Q ,< /0F J2 / 

 K '!   r < 0

  <F /0F J2 , , -. ' 6E  

   , -. 8; *   -.. O

  /0F J2 r 1 , . , -.

2/ ':/0
 < ,<
2/ 6"F ' /0 , U* J T , U  /'! >   *  )(-
/[ ' Z>  ,J 2/ ' 6"F /0 2E:.
<F /0F

M /0F
J 2/

2/

2.

]' [

]' ; J

]' ; J

]' [

2.

2/

J 2/

_-

_-

_-

_-

_


 /0F J2



 <2 E   * J  , -. 2  ! .  * >

>  J2   '! >  6"Fg  *  -.   -.  "*  -.


  -.i U 2< R   K$ *     , -."  T * i .
J2  0  -  T * !  , -. 5;E>g

SAS

:
SAS
SAS Statistical Analysis Software
SAS Institute Inc., Cary, NC,USA.

, SAS Main Frame
. SAS
. Program Editor, Log, Output,
: Program Editor .
EXL cards . SAS
: Log .
.
Program Editor
Recall text Run .
: Output . .
SAS

: Infile
Infile SAS Command file
. SAS data file
.
.Input Data .

) Dos
(.

: Cards
Cards

.
. )($
.
.
. ) (model
) (GLM, ANOVA, Regration.
.
.

F><Pr .
.

. Line LSD
.
.

Typ 1 Typ 3


Cards
;1. Options ls=72 nodate
;2. Data .
; 3. input
;)4. datalines or (cards
5.
)6. ; (semicolon
;7. proc means
8. proc means n nmiss mean std stderr clm min max sum
;var cv skewness kurtosis..
;9. run


Options .
DATA .
Input . )) Dollar ($
(

. cards

.

Input

. .
Proc means .
.
PROC .
:
*/ /* .

.
.
SAS . Exel

.
. SAS
Text .


.() . .
.() .
.

You might also like