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Variable selection and dimension reduction are major prerequisites for reliable multivariate regression analysis. Most a times, many variables used as independent variables in a multiple regression display high degree of correlations. This problem is known as multicollinearity. Absence of multicollinearity is essential for multiple regression models, because parameters estimated using multi-collinear data are unstable and can change with slight change in data, hence are unreliable for predicting the future. This paper presents the application of Principal Component Analysis (PCA) on the dimension reduction of milk composition variables. The application of PCA successfully reduced the dimension of the milk composition variables, by grouping the 17 milk composition variables into five principal components (PCs) that were uncorrelated and independent of each other, and explained about 92.38% of the total variation in the milk composition variables.

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Original Research

reduction of milk composition variables

Authors:

Alphonsus C1, Akpa GN1,

Nwagu BI2, Abdullahi I2,

Zanna M3, Ayigun AE3,

Opoola E3, Anos KU3,

Olaiya O3 and OlayinkaBabawale OI3

Institution:

1. Animal Science

Department, Ahmadu Bello

University, Zaria, Nigeria.

2. National Animal

Production Research

Institute, Shika-Zaria

3. Kabba College of

Agriculture, Ahmadu Bello

University, Kabba, Nigeria

ABSTRACT:

reliable multivariate regression analysis. Most a times, many variables used as

independent variables in a multiple regression display high degree of correlations. This

problem is known as multicollinearity. Absence of multicollinearity is essential for

multiple regression models, because parameters estimated using multi-collinear data

are unstable and can change with slight change in data, hence are unreliable for

predicting the future. This paper presents the application of Principal Component

Analysis (PCA) on the dimension reduction of milk composition variables. The

application of PCA successfully reduced the dimension of the milk composition

variables, by grouping the 17 milk composition variables into five principal

components (PCs) that were uncorrelated and independent of each other, and

explained about 92.38% of the total variation in the milk composition variables.

Corresponding author:

Alphonsus C

Keywords:

Principal component analysis, eigenvalues, communality

Email Id:

Article Citation:

Alphonsus C, Akpa GN, Nwagu BI, Abdullahi I, Zanna M, Ayigun AE, Opoola E,

Anos KU, Olaiya O and Olayinka-Babawale OI

Application of multivariate principal component analysis on dimensional reduction of

milk composition variables

Journal of Research in Biology (2014) 4(8): 1526-1533

Web Address:

http://jresearchbiology.com/

documents/RA0489.pdf

Dates:

Received: 27 Oct 2014

licenses/by/4.0), which gives permission for unrestricted use, non-commercial, distribution and

reproduction in all medium, provided the original work is properly cited.

Journal of Research in Biology

An International

Scientific Research Journal

www.jresearchbiology.com

used to reduce the number of predictive variables as well

INTRODUCTION

In recent times, many scientist, especially in the

2006)

composition variables

are highly correlated (Lovendahl et al., 2010; Alphonsus

Experimental site

Research

The

problem

with

multicollinearity

Yu, 2008).

is

that

Institute

(NAPRI)

Shika-Zaria,

located

it

grinded maize. They had access to water and salt lick ad-

et al., 2002).

Component

1527

The milk samples were frozen immediately after

o

Statistical Analysis

the

The

correlation

matrix

of

all

the

milk

same

characteristic

(http://support.sas.com/

publishing/publicat/chaps/55).

For

example,

milk composition

the

yield

With

the

coefficient

being

chosen

so

that

The measured milk composition variables were

1528

1529

0.070

dPLR

-0.061

-0.433

-0.388

0.021

0.000

-0.056

0.037

-0.669

0.044

0.853

0.019

-0.189

0.025

0.853

0.352

MFC

-0.391

-0.336

-0.002

0.187

0.117

0.120

0.232

0.162

0.169

-0.079

-0.089

-0.029

-0.054

0.305

MPC

0.147

0.017

-0.154

-0.084

-0.068

-0.085

-0.058

-0.889

-0.484

0.773

0.014

-0.275

-0.078

MLC

0.038

-0.254

-0.279

-0.671

-0.695

-0.714

-0.681

0.056

0.203

0.063

0.988

0.966

MFY

-0.005

-0.196

-0.183

-0.634

-0.666

-0.668

-0.645

0.272

0.218

0.191

0.943

MPY

0.115

-0.126

-0.220

-0.723

-0.734

-0.742

-0.728

-0.057

0.016

0.078

MLY

0.165

-0.284

-0.352

0.183

-0.118

-0.133

-0.095

-0.841

-0.048

FPR

-0.385

-0.691

-0.352

0.183

0.118

0.056

0.161

0.579

FLR

-0.363

0.171

-0.152

0.176

0.123

0.144

0.171

PLR

-0.297

-0.021

0.240

0.992

0.985

0.980

DMY

-0.23

0.142

0.345

0.983

0.989

dMFC

0.459

0.063

0.212

0.985

dMPC

-0.321

-0.036

0.246

dMLC

-0.427

0.605

dFPR

0.459

dFLR

milk composition variables indicated by the following: Average Daily Milk Yield (ADMY), Milk Fat Content (MFC), Milk Protein Content (MPC), Milk

Lactose Content (MLC), Milk Fat Yield (MFY), Milk Protein Yield (MPY), Milk Lactose Yield (MLY), Fat Protein Ratio (FPR), Fat Lactose Ratio (FLR),

Protein Lactose Ratio (PLR). Variable abbreviations starting with d are the current minus the previous values of milk measures in question. Yield values are

in kilogram per day (kg/day), content values are in percentages (%) and ratios are unitless. The measures used were group mean averages.

2

cummulative percentages of variation explained with increasing number of PC indicated

-0.129

dFLR

0.240

PLR

-0.182

0.183

FLR

dFPR

-0.177

FPR

-0.653

0.939

MLY

dMLC

0.986

MPY

-0.671

0.956

MFY

dMPC

-0.321

MLC

-0.674

-0.195

MPC

dMFC

-0.264

MFC

-0.669

ADMY

dMY

ADMY

*Milk

variables

Table 1: Correlation co-efficients among milk yield and milk composition variables used for prediction of Energy Balance (EB)

Table 2: Relationships among milk composition measures1 expressed as loadings in a

principal component analysis.

Items a

Principal components (PCs)

h

PC1

PC2

PC3

PC4

PC5

Variable explained2

38.88

60.01

75.00

85.30

92.38

Average Daily Milk Yield -0.34

-0.02

0.00

-0.00

99.81

0.93

(ADMY)

Milk Fat Content (MFC)

0.02

0.13

-0.23

0.42

99.96

0.85

Milk Protein Content (MPC)

-0.04

0.15

0.05

0.07

99.96

0.98

Milk Lactose Content (MLC)

0.05

0.13

0.08

0.37

99.89

0.82

Milk Fat Yield (MFY)

-0.33

0.17

-0.05

0.08

99.88

0.92

Milk Protein Yield (MPY)

-0.34

-0.01

-0.01

0.14

99.90

0.93

Milk Lactose Yield (MLY)

-0.34

0.19

0.01

0.07

99.83

0.91

Fat-Protein Ratio (FPR)

0.05

0.04

-0.27

-0.25

99.97

0.90

Fat-Lactose Ratio (FLR)

0.10

-0.04

-0.15

-0.48

-0.05

99.97

Protein-Lactose Ratio (PLR)

0.03

-0.06

-0.86

-0.09

0.17

99.86

dMY

-0.33

0.01

-0.06

0.01

99.40

0.94

dMFC

-0.32

-0.02

0.06

-0.03

99.77

0.94

dMPC

-0.32

0.02

-0.06

-0.04

88.81

0.94

dMLC

-0.31

-0.01

-0.07

-0.02

99.77

0.95

dFPR

-0.04

0.03

-0.25

0.04

99.94

0.81

dFLR

-0.04

-0.05

-0.08

-0.03

99.95

0.92

dPLR

-0.01

-0.09

0.22

0.02

-0.09

99.96

3

% variance

38.88

21.20

14.92

10.30

07.08

Eigen values

6.610 3.604

2.536 1.751

1.204

a

Variable abbreviations starting with d are the change variables signifying current minus

the previous values of milk measures in question. Yield values are in kilogram per day (kg/

day), content values are in percentages (%) and ratios are unitless.

2

cummulative percentages of variation explained with increasing number of PC indicated

3

percentage variance explained by each principal components

h= communality estimates is a variance in observed variables acounted for by a common

factor

subjected to Principal Component Analysis (PCA) using

(PC)

which

were

subsequently

labeled

change

1530

Table 3: Pearson correlation between the Principal components and milk composition variables

Variables i

Average daily milk yield

(ADMY)

Milk fat content (mFc)

Milk protein content (mPc)

PC1

PC2

PC3

-0.340

0.938**

-0.016

PC

0.000

PC5

0.004

0.018

-0.043

0.135

0.146

0.853**

0.059

-0.233

0.015

0.317

0.981**

Milk fat yield (mFy)

-0.052

-0.327

0.128

0.923**

0.825

0.168

0.085

-0.053

0.373

0.079

-0.341

0.928**

0.012

-0.005

0.137

10.342

0.909**

0.193

0.014

0.078

0.046

0.039

0.900**

-0.267

-0.246

Fat-lactose ratio (FLR)

0.098

-0.036

-0.153

-0.476

-0.046

Protein-lactose ratio (PLR)

0.029

-0.061

-0.859**

-0.085

0.172

dmy

0.939**

-0.328

0.008

-0.057

0.009

dmFc

0.942**

-0.322

-0.021

0.069

-0.030

dmPc

0.941**

-0.316

0.021

-0.062

-0.039

dmLc

0.944**

-0.307

-0.008

-0.069

-0.022

dFPR

-0.041

0.027

-0.254

0.811**

0.043

dFLR

-0.044

-0.055

-0.082

0.921**

-0.028

dPLR

-0.005

-0.091

0.221

0.049

-0.087

PC1

1.000

0.000

0.000

0.000

0.000

PC2

0.000

1.000

0.000

0.000

0.000

PC3

0.000

0.000

1.000

0.000

0.000

PC4

0.000

0.000

0.000

1.000

0.000

PC5

0.000

0.000

0.000

0.000

1.000

I

Variable abbreviations starting with d are the current minus the previous values of milk measures in

question. Yield values are in kilogram per day (kg/day), content values are in percentages (%) and ratios are unitless. The measures used were group mean averages. ** = P < 0.001

on it, suggesting that MPC is not strongly correlated with

explained larger amount of variation (38.88%) among

The

PCs

displayed

varying

degrees

of

correlation among the PCs was zero. This shows that the

1531

Table 4: Descriptive statistics of the principal components

Principal components

N

Means

S.D

Min

(PCs)

PC1

60

0.00

1.000

-2.544

PC2

60

0.00

1.000

-3.001

PC3

60

0.00

1.000

-2.626

PC4

60

0.00

1.000

-5.045

PC5

60

0.00

1.000

-4.104

Max

3.102

2.573

2.036

2.563

2.085

uncorrelated and independent of each other. Also, the

Animal

Science

Tibshirani. 2006. Prediction by supervised Principal

CONCLUSION

The Principal Component Analysis (PCA)

successfully reduced the dimensionality of the milk

Association. 473 (19): 119-137.

be used to solve the problem of multicollinearity and

variable reduction in multiple regression analysis

fertility. University of Melbourne, Department of

Veterinary Science, VIAS, Sneydes Road 600, Werribee,

Victoria,

REFERENCES

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post-partum

reproductive

function

using

Central

milk

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Web

link:

http://

w w w . n h i a . o r g . a u / h t m l /

body_milk_protein__fertility.html 30/10/2008.

estimates amongst milk yield and milk composition

characteristics of Bunaji and Friesian Bunaji cows.

African Journal of Biotechnology. 11(36): 8790-8793.

Alphonsus C, Akpa GN, Nwagu BI, Barje PP,

Orunmuyi M, Yashim SM, Zana M, Ayigun AE and

Opoola E. 2013. Evaluation of Nutritional Status of

Friesian

x Bunaji

Dairy Herd

Based

on Milk

Newton Square PA: United States Department of

Agriculture.

Forest

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1-48p

Web

link:

www.fs.fed.us/ne/morgantown/4557/dendrochron/

rpne721.pdf.

Friggens NC, Ridder C and Lvendahl P. 2007. On

the use of milk composition measures to predict the

energy balance of dairy cows. Journal of Dairy Science.

90(12): 5453-5467

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Hansen LB. 2000. Consequences of selection for milk

yield from a geneticist's viewpoint. Journal of Dairy

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Malau-Aduli AEO, Alawa CBI and Lamidi OS. 2001.

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Ingvartsen KL, Dewhurst RJ and Friggens NC. 2003.

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