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Generalised Procrustes Analysis - OP&P Product Research

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<strong>Generalised</strong> <strong>Procrustes</strong><br />

<strong>Analysis</strong><br />

applications in sensory evaluation and<br />

instrumental analysis


GPA course, ©OP&P <strong>Product</strong> <strong>Research</strong>,<br />

Utrecht<br />

Senstools ® is an OP&P trademark<br />

It is not allowed to copy or use parts of this<br />

course without proper reference to OP&P<br />

Utrecht, 2004<br />

<strong>Procrustes</strong> principles


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data, different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program


• The history of GPA<br />

Introduction<br />

• Description of the Senstools package:<br />

functionality and tools<br />

• GPA routine in Senstools<br />

Introduction


History of GPA<br />

• 1952 (Green), 1962 (Hurley & Cattel): onesided<br />

orthogonal <strong>Procrustes</strong> rotation<br />

• 1968 (Schönemann), 1970 (Schönemann &<br />

Carroll): two-sided orthogonal <strong>Procrustes</strong><br />

rotation with scaling<br />

• 1971 (Wingersky): more than two<br />

configurations<br />

Introduction: history GPA


History: continued<br />

• 1975 (Gower): generalised <strong>Procrustes</strong> with<br />

scaling factor and Anova (Psychometrika)<br />

• 1982-1986: practical application in sensory<br />

by Tony Williams, Gillian Arnold, Steve<br />

Langron and others<br />

• until 1989 GPA was only available as macro<br />

in SAS or Genstat<br />

Introduction: history GPA


History: continued<br />

• 1989: OP&P wrote the first PC routine for<br />

GPA in APL (<strong>Procrustes</strong>-PC)<br />

• 1993: the program was written in C<br />

• 1995: Senstools-for-Windows v1.0 was<br />

released<br />

• 2000: Senstools v3.0 was released<br />

Introduction: history GPA


Time needed to solve a simple<br />

problem<br />

20 subjects - 8 products - 20 attributes<br />

1989 13 hours<br />

1993 25 minutes<br />

1995 55 seconds<br />

2000 0,6 seconds<br />

Introduction: history GPA


Description of Senstools package<br />

Data analysis tool for sensory professionals<br />

Uni- and multivariate statistics<br />

• descriptive statistics<br />

• analysis of variance<br />

• assessor statistics and concordance<br />

Introduction: Senstools package


• PCA<br />

Description continued….<br />

• Generalized <strong>Procrustes</strong> <strong>Analysis</strong><br />

• MDPref<br />

• Latent Variable Cluster analysis<br />

• Graphics<br />

Introduction: Senstools package


GPA routine in Senstools<br />

Introduction: Senstools package


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data, different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program


<strong>Procrustes</strong><br />

• <strong>Procrustes</strong> was a character of Greek myth.<br />

An innkeeper who plied his trade in Attica,<br />

he put his victims on an iron bed. If they<br />

were longer than the bed, he cut off their<br />

feet. If they were shorter, he stretched<br />

them……..<br />

<strong>Procrustes</strong> principles


More or less like this….<br />

<strong>Procrustes</strong> principles


The Procrustean principles<br />

Make the configurations fit each other:<br />

• do this by moving them to a common origin<br />

• stretch or shrink each configuration in order<br />

to make it fit as good as possible<br />

• if needed, flip them around<br />

<strong>Procrustes</strong> principles


in summary:……..<br />

• <strong>Procrustes</strong> only allows ‘rigid-body’ transformations<br />

to the datasets<br />

• these transormations respect the relative<br />

distances between objects<br />

<strong>Procrustes</strong> principles


Modern Proctustes<br />

• consider K configurations of n objects in pdimensional<br />

spaces<br />

• how can we represent the K configurations<br />

in a common space while minimizing the<br />

goodness of fit criterion?<br />

• we do this with the aid of 3 transformations<br />

<strong>Procrustes</strong> principles


translation<br />

The first transformation<br />

• move the centroids of each configuration to<br />

a common origin<br />

<strong>Procrustes</strong> principles


3 sets (A,B,C)<br />

3 products (1,2,3)<br />

2 attributes<br />

A2<br />

A1<br />

Set A<br />

B1<br />

<strong>Procrustes</strong> principles<br />

C1<br />

B2<br />

A3<br />

Set B<br />

B3<br />

Set C<br />

C2<br />

C3


sets translated to<br />

common origin<br />

C1<br />

<strong>Procrustes</strong> principles<br />

A2<br />

B1<br />

A1<br />

C2<br />

B2<br />

B3<br />

A3<br />

C3


The second transformation<br />

isotropic scaling<br />

• shrink or stretch each configuration<br />

isotropically to make them as similar as<br />

possible<br />

<strong>Procrustes</strong> principles


sets isotropically<br />

scaled<br />

B1<br />

C1<br />

A2<br />

<strong>Procrustes</strong> principles<br />

A1<br />

C2<br />

B2<br />

A3<br />

B3<br />

C3


The third transformation<br />

rotation/reflection<br />

• turn or flip the configurations<br />

<strong>Procrustes</strong> principles


The notation and algorithm<br />

<strong>Procrustes</strong> principles


1.1 Notation<br />

T Transformation matrix, in GPA context a rotation matrix: T'T’=T’T'=I<br />

X a 3-way or K-sets datamatrix of order K×N×M (3-way, K individual data sets of N rows×M<br />

colums) or K×N×Mk (K-sets)<br />

X the group average matrix K<br />

− K<br />

1<br />

k=<br />

1<br />

Xk a group average matrix excluding Xk from the average:<br />

X<br />

k<br />

T<br />

k<br />

X<br />

k<br />

−1<br />

K<br />

Xi<br />

i<br />

i=<br />

1,<br />

i≠k<br />

= ( K −1)<br />

T<br />

Y a 2-way matrix of order (N×J), of design variables and/or physical/chemical variables.<br />

1.2 Algorithm<br />

The GPA method was first described by Gower (1975), and some modifications are found in Ten<br />

Berge (1977). We will follow the algorithm as basically provided by the latter. It is convenient to<br />

interpret the algorithm to consist of three main parts (see Fout! Verwijzingsbron niet gevonden.):<br />

1. Pre-processing and initialisation<br />

2. Procrustean iterations, possibly including isotropic scaling<br />

3. Post processing and presentation of results<br />

All three parts are potentially subject to adaptation due to our inclusion of a PLSR step to allow for<br />

an extra Y matrix to exert its influence. For the moment we will envision a PLSR step to be<br />

included in step 2 above. The original GPA algorithm according to Ten Berge (1977) is as follows,<br />

ignoring for the moment pre- and post-processing steps, which are not part of the GPA process<br />

proper.<br />

Initialisation of the necessary parameters.<br />

For k=1, …, K rotate Xk to k X by T = QP′<br />

, where P and Q come from the SVD<br />

′ k k<br />

X X = P Q′<br />

Evaluate the loss function: σ =<br />

s<br />

K<br />

k=<br />

1<br />

X T − X<br />

k<br />

k<br />

<strong>Procrustes</strong> principles<br />

PRE-PROCESSING<br />

Translation<br />

PCA on long individual sets<br />

Scaling the total variation<br />

INITIALISATION<br />

Initializing rotation matrices on I<br />

Initializing scaling factors on 1<br />

ROTATION<br />

set loop k=1,…,K<br />

SCALING<br />

set loop k=1,...,K<br />

CONVERGENCE TEST<br />

σ s -σ s-1


Basic principles of GPA<br />

• Use the 3 transformations to make the<br />

individual spaces as similar as possible<br />

• Compute a Group-Average-Space of these<br />

individual spaces<br />

• Compute the difference between the Group<br />

and Individual spaces (the residuals)<br />

• Minimizes the total residual by applying the<br />

3 transformations<br />

<strong>Procrustes</strong> principles


The computations<br />

• GPA performs the transformations on each set<br />

• Individual configurations are averaged when<br />

they are as alike as possible<br />

• the resulting high-dimensional space is reduced<br />

by means of PCA to a lower dimensionality<br />

• the total variance in the data is partitioned over<br />

sets, objects or dimensions<br />

<strong>Procrustes</strong> principles


<strong>Procrustes</strong>-Anova (Panova)<br />

• The total variance (V T ) consists of consensus<br />

variance (V C ) and within variance (V W )<br />

• the consensus variance (V C ) consists of two<br />

parts: the part explained by the first Q<br />

dimensions of the consensus space (V I ) and the<br />

part left unexplained (V O , the part associated<br />

with the higher dimensions)<br />

<strong>Procrustes</strong> principles


The <strong>Procrustes</strong>-Anova (Gower)<br />

Zero padding assym. data<br />

and centering<br />

V T<br />

Scaling and rotation<br />

Averaging individual spaces<br />

V C=(V T-V W)<br />

PCA to lower dim. space<br />

V I=(V T-V W -V O)<br />

<strong>Procrustes</strong> principles<br />

Loss V W<br />

Loss V O<br />

Group<br />

average<br />

space


Panova output in Senstools<br />

• The total, consensus and residual variance is<br />

shown as it is distributed over sets, objects and<br />

dimensions<br />

• high consensus variance for objects indicates<br />

agreement about the position of the objects by<br />

the assessors<br />

• high residual variance for assessors indicate<br />

that the assessor does not agree with the others<br />

<strong>Procrustes</strong> principles


Significance of the results ?<br />

• in contrast with PCA, the amount of variance<br />

explained in itself does not give an indication<br />

for the significance or fit of the final solution<br />

• a permutation test is used to estimate the odds<br />

that a ‘random’ dataset would give a similar<br />

percentage consensus variance<br />

<strong>Procrustes</strong> principles


The <strong>Procrustes</strong> permutation test<br />

• take the original dataset, permute the rows<br />

within each set and run an analysis<br />

• repeat this 50 times<br />

• the 90th and 98th percentile of the percentage<br />

of consensus variance from these permuted<br />

sets are compared to the percentage in the<br />

actual dataset<br />

<strong>Procrustes</strong> principles


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data, different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program


• 3-mode data<br />

Two basic types of data<br />

– products×assessor×characteristics<br />

– (conventional) profiling<br />

• K-sets data<br />

– products×(assessors×idiosyncratic characteristics)<br />

– ‘free choice’ profiling<br />

Different data


N products<br />

M attributes<br />

3 Mode data<br />

Different data<br />

K assessors<br />

( N × M ) datamatrix X k<br />

for one assessor<br />

3-mode data structure representing Conventional Profiling data: N<br />

products are judged by K assessors using M attributes.


N products<br />

X<br />

1<br />

M 1 attributes<br />

K-sets data<br />

X<br />

2<br />

M 2 attributes<br />

K assessors<br />

X<br />

3<br />

M 3 attributes<br />

Data structure representing Free Choice Profiling data: N products are judged<br />

by K assessors each using M k attributes.<br />

Different data<br />

X<br />

K<br />

M K attributes


Averaging sensory data<br />

• Conventional profiling: we can average and<br />

use PCA to summarize<br />

• FCP: we cannot average, we need GPA<br />

• in case of individual differences, can we<br />

average at all?<br />

Different data


ΣΣ.. results in averaged data set<br />

<strong>Product</strong>s<br />

attributes 1-n<br />

Average<br />

Different data<br />

Analyses:<br />

PCA/Factor<br />

MDS<br />

…...


PCA<br />

• Fit a low dimensional structure that captures<br />

the most variance of the high dimensional<br />

structure<br />

• shows (cor)relations between variables<br />

• shows similarities between objects<br />

• gives fit of dimensions<br />

see Jolliffe, I.T. (1986). Principal Component <strong>Analysis</strong>. Springer-Verlag.<br />

Different data


Correlation matrix<br />

PRED PGREEN MOIST DRYMAT ACID ITHICK KATAC<br />

PRED 1.000<br />

PGREEN 0.921 1.000<br />

MOIST 0.841 0.846 1.000<br />

DRYMAT 0.196 0.098 0.027 1.000<br />

ACID 0.609 0.526 0.502 0.534 1.000<br />

ITHICK 0.224 0.182 0.361 0.327 0.390 1.000<br />

KATAC -0.609 -0.587 -0.669 -0.207 -0.497 -0.301 1.000<br />

Instrumental measurements on 66 apples.<br />

Different data


%VAF<br />

60<br />

50<br />

40<br />

30<br />

20<br />

10<br />

0<br />

55.883<br />

Scree graph<br />

19.286<br />

10.756<br />

Different data<br />

6.834<br />

4.51<br />

1.707<br />

1 2 3 4 5 6 7<br />

Dimension<br />

1.024


dimension 2<br />

0.8<br />

0.6<br />

0.4<br />

0.2<br />

0<br />

-0.2<br />

-0.4<br />

-0.6<br />

Biplot<br />

DRYMAT<br />

ITHICK<br />

ACID<br />

15<br />

18<br />

KATAC<br />

6 30<br />

9<br />

19 7<br />

226<br />

+<br />

35 29 2021 23<br />

22<br />

14 17<br />

24<br />

31<br />

3275<br />

8<br />

2834<br />

12<br />

1 10<br />

25<br />

33<br />

32<br />

13<br />

11 4<br />

PRED<br />

MOIST<br />

16 PGREEN<br />

36<br />

54<br />

63<br />

62<br />

6647<br />

57 5641<br />

64<br />

71<br />

44 58<br />

65<br />

72<br />

69 6042 38<br />

55<br />

5345<br />

59<br />

61<br />

68<br />

48 39 50 51<br />

43 40 67<br />

46<br />

49<br />

70<br />

52<br />

37<br />

-0.8<br />

-0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8<br />

dimension 1


Applications of GPA -1<br />

Why use GPA instead of PCA for conventional<br />

profiling?<br />

• GPA will preserve the individual information:<br />

- information about individual scale-usage<br />

- the relative contribution of individuals to the<br />

group result<br />

- the consensus of individuals with the group<br />

GPA in Sensory


Applications of GPA -2<br />

The special case: non-matching attributes<br />

• GPA is the only way to analyze:<br />

- data from different countries/languages<br />

- free choice profiling data<br />

- in general: K Sets data<br />

GPA in Sensory


Format of free choice data<br />

<strong>Product</strong>s<br />

attributes set 1<br />

Set 1<br />

Set 2<br />

GPA in Sensory<br />

only products are similar<br />

attributes set 2 attributes set 3 ributes set 4<br />

Set 3<br />

Set 4<br />

utes set K<br />

attributes set 5<br />

Set K


<strong>Product</strong>s<br />

Format of K Sets data<br />

chemical data<br />

Chemical<br />

GPA in Sensory<br />

attributes<br />

instrumental data<br />

Instrumental<br />

only products are similar<br />

Sensory


GPA in sensory & consumer<br />

science - 1<br />

GPA in sensory science:<br />

• shows the relationships between products and<br />

attributes<br />

• monitoring panelist performance<br />

• relating sensory data to instrumental or<br />

chemical data<br />

GPA in Sensory


GPA in sensory & consumer<br />

science - 2<br />

GPA in consumer science:<br />

• shows the relationships between products and<br />

attributes<br />

• takes individual differences into account<br />

• corrects for lack of training<br />

GPA in Sensory


Basic assumptions in classical<br />

sensory profiling<br />

• assessors know meaning of attributes<br />

• assessors know meaning of scale<br />

• assessors use scale in consistent manner<br />

Training will provide the necessary skills !<br />

GPA in Sensory


Nevertheless: three possible<br />

• Effects of level<br />

• Effects of range<br />

problems<br />

• Effects of meaning/interpretation<br />

GPA in Sensory


Effects of level<br />

Very weak Very strong<br />

assessor 1<br />

Very weak Very strong<br />

assessor 2<br />

GPA in Sensory


Effects of range<br />

Very weak Very strong<br />

Very weak Very strong<br />

GPA in Sensory


Effects of meaning/interpretation<br />

Very weak sweetness Very strong<br />

Very weak bitterness Very strong<br />

GPA in Sensory


GPA removes the effects of level, range and<br />

interpretation from each individual dataset by<br />

applying 3 transformations:<br />

- translation to common mean<br />

- isotropic scaling (stretch or shrink)<br />

- rotation/reflection<br />

In summary:<br />

GPA in Sensory


FCP or Sensory-Instrumental<br />

relations<br />

• in these situations, we can not average<br />

• ‘attributes’ have different meanings for each<br />

set and each set can have different numbers<br />

of attributes<br />

• still, we want to find a common, underlying<br />

structure<br />

GPA in FCP


The ‘FCP’ principles:<br />

• GPA allows us to match different configurations<br />

without assumptions about the axis<br />

• these configurations are made as similar as<br />

possible by using the 3 transformations<br />

• on the basis of the individual spaces, a group<br />

space is computed in which the ‘attributes’<br />

from each individual space are projected<br />

GPA in FCP


Other methods to relate Sensory -<br />

Instrumental data<br />

• assymetric methods (try to predict one set<br />

from another)<br />

for example: PLS, PCR, MulReg<br />

• symmetric methods (only relations between<br />

sets are studied)<br />

for example: CCA, GPA<br />

<strong>Procrustes</strong> principles


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data - different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program


The classical example: beef data<br />

from Gower<br />

• 3 judges rated 9 beef carcasses with respect<br />

to 7 different attributes (k=3, m=7 and n=9)<br />

• this results in 3 matrices of 9 x 7 data points<br />

• first: descriptives<br />

<strong>Procrustes</strong> principles


Averaged rating and standard<br />

deviation by judge (63 obs)<br />

Mean StdDev<br />

J2 38 16<br />

J1 51 18<br />

J3 53 28<br />

<strong>Procrustes</strong> principles


Judge#1 by attributes and carcasses<br />

Spiderplot: attributes over objects (J1)<br />

carc8<br />

carc6<br />

carc5<br />

carc7<br />

carc4<br />

carc3<br />

<strong>Procrustes</strong> principles<br />

carc9<br />

carc2<br />

carc1<br />

att1<br />

att2<br />

att3<br />

att4<br />

att5<br />

att6<br />

att7<br />

mean rating: 51<br />

St. dev.: 18


Judge#3 by attributes and carcasses<br />

Spiderplot: attributes over objects (J3)<br />

carc8<br />

carc6<br />

carc5<br />

carc7<br />

carc4<br />

carc3<br />

<strong>Procrustes</strong> principles<br />

carc9<br />

carc2<br />

carc1<br />

att1<br />

att2<br />

att3<br />

att4<br />

att5<br />

att6<br />

att7<br />

mean rating: 53<br />

St. dev.: 28


Averaged rating and standard<br />

deviation by carcass (27 obs)<br />

carc8 carc1 carc3 carc4 carc5 carc7 carc2 carc6 carc9<br />

Mean 31 40 41 43 45 52 53 60 64<br />

StdDev 28 8 21 20 22 18 20 20 19<br />

<strong>Procrustes</strong> principles


Carcass #1 by judges and attributes<br />

Spiderplot: sets over attributes (carc1)<br />

att6<br />

att5<br />

att4<br />

att3<br />

<strong>Procrustes</strong> principles<br />

att7<br />

att2<br />

att1<br />

J1<br />

J2<br />

J3<br />

mean rating: 53<br />

St. dev.: 28


Carcass #3 by judges and attributes<br />

Spiderplot: sets over attributes (carc3)<br />

att6<br />

att5<br />

att4<br />

att3<br />

<strong>Procrustes</strong> principles<br />

att7<br />

att2<br />

att1<br />

J1<br />

J2<br />

J3<br />

mean rating: 53<br />

St. dev.: 28


Averaged rating and standard<br />

deviation by attribute (21 obs)<br />

att7 att1 att6 att4 att5 att3 att2<br />

Mean 35 41 43 43 51 55 64<br />

StdDev 8 22 22 26 23 20 16<br />

<strong>Procrustes</strong> principles


Attribute #7 by judges and carcasses<br />

Spiderplot: sets over objects (att7)<br />

carc6<br />

carc5<br />

carc7<br />

carc4<br />

carc8<br />

carc3<br />

<strong>Procrustes</strong> principles<br />

carc9<br />

carc2<br />

carc1<br />

J1<br />

J2<br />

J3<br />

mean rating: 35<br />

St. dev.: 8


Attribute #4 by judges and carcasses<br />

Spiderplot: sets over objects (att4)<br />

carc6<br />

carc5<br />

carc7<br />

carc4<br />

carc8<br />

carc3<br />

<strong>Procrustes</strong> principles<br />

carc9<br />

carc2<br />

carc1<br />

J1<br />

J2<br />

J3<br />

mean rating: 43<br />

St. dev.: 26


Univariate results<br />

• the carcasses differ on 5 out of 7 attributes<br />

• the judges differ in level and range effect<br />

• there is very little variation in the rating of<br />

carcass 1 and in the use of attribute 7<br />

NOW, LET’S PROCRUSTES<br />

<strong>Procrustes</strong> principles


Scree plot - Gower data<br />

<strong>Procrustes</strong> principles


Panova table<br />

Real Residual Total<br />

Dim 1 60,9 13,2 74,1<br />

Dim 2 8,1 2,4 10,5<br />

Dim 3 6,4 2,5 8,9<br />

Dim 4 2,7 1,0 3,7<br />

Dim 5 1,2 0,4 1,6<br />

Dim 6 0,4 0,2 0,6<br />

Dim 7 0,3 0,3 0,6<br />

Total 80,1 19,9 100,0<br />

<strong>Procrustes</strong> principles


0.25<br />

0.20<br />

0.15<br />

0.10<br />

0.05<br />

0.00<br />

Explained (real) variance by object<br />

Real Variance by Object<br />

carc1 carc2 carc3 carc4 carc5 carc6 carc7 carc8 carc9<br />

<strong>Procrustes</strong> principles<br />

Dim 4<br />

Dim 3<br />

Dim 2<br />

Dim 1


0.08<br />

0.06<br />

0.04<br />

0.02<br />

0.00<br />

Residual by judge<br />

Residual Variance by Set<br />

J1 J2 J3<br />

Data Gower, Psychometrica 1975<br />

<strong>Procrustes</strong> principles


Group average space and individual sets<br />

GPA Group Average : dimension 1 versus 2<br />

J3<br />

3,59<br />

-3,59<br />

J1<br />

carc8 J2<br />

J1<br />

carc1<br />

J2 J3<br />

J1<br />

carc5<br />

J2<br />

J2<br />

carc3 J2 J1 carc2 J1<br />

J1<br />

J3 carc4 carc7<br />

J3<br />

J2<br />

J2 J3<br />

J2<br />

carc6<br />

J3 J3<br />

J1 J1<br />

J1 carc9<br />

J3<br />

3,59<br />

J3<br />

J2<br />

-3,59<br />

<strong>Procrustes</strong> principles


Group space with averaged attributes<br />

GPA Group Average : dimension 1 versus 2<br />

carc1<br />

3,59<br />

carc5<br />

carc6<br />

att1 att7<br />

-3,59 carc3<br />

carc2 att5 att6<br />

3,59<br />

carc4 carc7<br />

att4<br />

carc8<br />

att3<br />

carc9<br />

att2<br />

-3,59<br />

<strong>Procrustes</strong> principles


Permutation Results:<br />

Permutation test<br />

Total VAF in Real Data Set : 80,1 at 0 %<br />

Upper 10 % of the TVA in the permutated<br />

data Sets : 69,2<br />

Upper 5 % of the TVA in the permutated<br />

data Sets : 71,8<br />

<strong>Procrustes</strong> principles


PCA on averaged dataset<br />

PCA Results (Correlation) : dimension 1 versus 2<br />

2,97<br />

carc1<br />

carc2<br />

carc3<br />

-2,97<br />

att1<br />

att6 att7<br />

att5<br />

carc6 att4<br />

carc5carc4<br />

2,97<br />

carc9<br />

carc7 carc8<br />

att2 att3<br />

-2,97<br />

<strong>Procrustes</strong> principles


How similar are the results?<br />

• compare n-dim PCA space with n-dim GPA<br />

space<br />

• this is a 2-set GPA problem (‘free choice’)<br />

can the two [m x n] sets be fitted into a<br />

common group space?<br />

<strong>Procrustes</strong> principles


Group space for the two datasets<br />

GPA Group Average : dimension 1 versus 2<br />

PCA<br />

carc1<br />

2,95<br />

PCA<br />

carc5<br />

GPA<br />

PCA carc6<br />

GPA<br />

-2,95<br />

GPA carc4<br />

PCA<br />

carc7<br />

GPA<br />

2,95<br />

GPA<br />

carc8<br />

PCA<br />

PCA<br />

PCA<br />

carc9<br />

GPA<br />

PCA<br />

GPA<br />

GPAcarc3<br />

PCA carc2 GPA<br />

-2,95<br />

<strong>Procrustes</strong> principles


Is this result significant?<br />

Permutation Results:<br />

Total VAF in Real Data Set : 82,8 at 4 %<br />

Upper 10 % of the TVA in the permutated<br />

data Sets : 82,4<br />

Upper 5 % of the TVA in the permutated<br />

data Sets : 82,7<br />

<strong>Procrustes</strong> principles


Another sensory example<br />

• the data are collected by Michael Bom Frøst,<br />

Ph.D. student Sensory Science Group -<br />

Department of Dairy and Food Science, KVL,<br />

Denmark<br />

<strong>Procrustes</strong> principles


• 7 judges<br />

The dataset<br />

• 16 different milk samples (triplicated)<br />

• 23 sensory attributes<br />

<strong>Procrustes</strong> principles


Questions to be answered<br />

• are there differences between the products<br />

• are the judges consistent<br />

• how can we characterize the products<br />

<strong>Procrustes</strong> principles


Are there differences between the products?<br />

80<br />

60<br />

40<br />

20<br />

ANOVA : F Ratios by Attribute<br />

0<br />

Cream-smell Whiteness Blueness Glass coating Cream-flavour Sweet Creaminess-oral Overal fattiness<br />

Boiled milk-smell Yellowness Transparency Thickness-visual Boiled milk-fla Thickness-oral Residual mouth feel<br />

<strong>Procrustes</strong> principles


Are there differences between the products?<br />

• yes, very clear differences for each attribute<br />

• the most outspoken difference is for ‘glass<br />

coating’<br />

• the least outstanding difference is for<br />

‘boiled milk’ and ‘sweet’<br />

<strong>Procrustes</strong> principles


Are there judges consistent?<br />

Agreement Between Assessors (Correlations)<br />

5<br />

4<br />

3<br />

2<br />

1<br />

-1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1<br />

<strong>Procrustes</strong> principles


Are there judges consistent?<br />

• yes, there is a very good correlation<br />

between each judge and the group average<br />

without that judge<br />

• inspect also the assessor statistics of the<br />

repeated measures anova (ratio of variance<br />

between products and within replications<br />

for each assessor and attribute)<br />

<strong>Procrustes</strong> principles


50<br />

40<br />

30<br />

20<br />

10<br />

0<br />

Are there judges consistent?<br />

RANOVA Assessor Statistics F Ratios by Attribute<br />

set 1 set 2 set 3 set 4 set 5 set 6 set 7<br />

<strong>Procrustes</strong> principles<br />

Cream-smell<br />

Boiled milk-smell<br />

Whiteness<br />

Yellowness<br />

Blueness<br />

Transparency<br />

Glass coating<br />

Thickness-visual<br />

Cream-flavour<br />

Boiled milk-fla<br />

Sweet<br />

Thickness-oral<br />

Creaminess-oral<br />

Residual mouth feel<br />

Overal fattiness


50<br />

40<br />

30<br />

20<br />

10<br />

0<br />

A different look<br />

RANOVA Assessor Statistics F Ratios by Assessor<br />

Cream-smell Whiteness Blueness Glass coating Cream-flavour Sweet Creaminess-oral Overal fattiness<br />

Boiled milk-smell Yellowness Transparency Thickness-visual Boiled milk-fla Thickness-oral Residual mouth feel<br />

<strong>Procrustes</strong> principles<br />

set 1<br />

set 2<br />

set 3<br />

set 4<br />

set 5<br />

set 6<br />

set 7


GPA group space with products and attributes<br />

GPA Group Average : dimension 1 versus 2<br />

1,63<br />

-1,63<br />

M1<br />

M3<br />

M2 M15<br />

Glass coating Yellowness M4<br />

M16<br />

M6<br />

Overal fattiness<br />

Whiteness<br />

M5 M7<br />

Cream-flavour<br />

Sweet<br />

Cream-smell<br />

M8<br />

M9<br />

M12<br />

Boiled milk-fla<br />

M11 Blueness<br />

Transparency M13<br />

M14 M10<br />

1,63<br />

-1,63<br />

<strong>Procrustes</strong> principles


Relation between attributes and products<br />

• the solution is almost uni-dimensional (dim<br />

1 explains 74% and dim 2 only 4%)<br />

• the major distinction is based on fattiness<br />

and creaminess versus color and transparancy<br />

<strong>Procrustes</strong> principles


A third example<br />

Expert data - sensory profiles<br />

• 15 different tomato soups are rated by 14<br />

experts on 25 attributes<br />

• soups vary in type (can, glass, instant and<br />

freshly made)<br />

<strong>Procrustes</strong> principles


Are there differences between the products?<br />

150<br />

100<br />

50<br />

0<br />

ANOVA F Ratios by Attribute<br />

saltt sweet taste int broth creamy thick mf sticky mf aftert color thickness coarseness nat. odor broth odor<br />

sour bitter fullness spicy mealy fatty mf crunchy metal taste tapioca filling odor full odor<br />

<strong>Procrustes</strong> principles


Are there differences between the products?<br />

• yes, very clear differences for each attribute<br />

• the most outspoken difference is for ‘tapioca’<br />

<strong>Procrustes</strong> principles


Expert data - sensory profiles<br />

Agreement Between Assessors (Correlations)<br />

8<br />

6<br />

4<br />

2<br />

-1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1<br />

<strong>Procrustes</strong> principles


Are there judges consistent?<br />

• yes, there is a very good correlation between<br />

each judge and the group average without that<br />

judge (except for one judge)<br />

• assessor statistics<br />

<strong>Procrustes</strong> principles


200<br />

150<br />

100<br />

50<br />

0<br />

Are there judges consistent?<br />

RANOVA Assessor F Ratios by Attribute<br />

set 1 set 2 set 3 set 4 set 5 set 6 set 7 set 8 set 9 set 10 set 11 set 12 set 13 set 14<br />

<strong>Procrustes</strong> principles<br />

saltt<br />

sour<br />

sweet<br />

bitter<br />

taste int<br />

fullness<br />

broth<br />

spicy<br />

creamy<br />

mealy<br />

thick mf<br />

fatty mf<br />

sticky mf<br />

crunchy<br />

aftert<br />

metal taste<br />

color<br />

tapioca<br />

thickness<br />

filling<br />

coarseness<br />

odor<br />

nat. odor<br />

full odor<br />

broth odor


Permutation Results:<br />

Permutation test<br />

Total VAF in Real Data Set : 81,3 at 0 %<br />

Upper 10 % of the TVA in the permutated<br />

data Sets : 54,9<br />

Upper 5 % of the TVA in the permutated<br />

data Sets : 55,0<br />

<strong>Procrustes</strong> principles


1.0<br />

0.8<br />

0.6<br />

40,6%<br />

0.4<br />

0.2<br />

Expert data - dimensionality<br />

57,4%<br />

70,4%<br />

Screeplot<br />

77,4%<br />

<strong>Procrustes</strong> principles<br />

82,6% 87,5%<br />

90,9% 93,5%<br />

0.0<br />

dim 1 dim 2 dim 3 dim 4 dim 5 dim 6 dim 7 dim 8


GPA Group Average : dimension 1 versus 2<br />

Expert data - all attributes<br />

1,14<br />

-1,14 Can/cream<br />

Can5<br />

Froz/cream<br />

Frozen1<br />

Can2 broth<br />

Can4<br />

fatty mf saltt Can1<br />

broth odor<br />

Fresh<br />

Can3<br />

1,14<br />

Can/cream4<br />

Can/cream2<br />

creamy mealysticky<br />

mf sweet<br />

metal taste<br />

HomeMade<br />

bitter<br />

odor<br />

crunchy<br />

color spicy<br />

fullness full<br />

nat. Standard odor tapioca<br />

odor coarseness filling<br />

sour aftert taste int<br />

Glass1<br />

thick mf<br />

thickness<br />

Instant1<br />

-1,14<br />

<strong>Procrustes</strong> principles


0.15<br />

0.10<br />

0.05<br />

0.00<br />

Expert data - explained variance<br />

Real Variance by Object<br />

Can1 HomeMade Can2 Can/cream2 Glass1 Can4 Can/cream4 Can5<br />

Can/cream Frozen1 Froz/cream Can3 Fresh Instant1 Standard<br />

<strong>Procrustes</strong> principles<br />

Dim 3<br />

Dim 2<br />

Dim 1


Expert data: individual performance<br />

• GPA allows us to inspect the performance<br />

of individuals in the group average space<br />

• in the case of experts or trained panels, the<br />

variability between individuals should be<br />

low<br />

so, let’s see<br />

<strong>Procrustes</strong> principles


Expert data - attribute tapioca<br />

GPA Group Average : dimension 1 versus 2<br />

1,14<br />

Froz/cream<br />

Can5 Frozen1<br />

Can2<br />

Can4<br />

Can1<br />

-1,14 Can/cream1<br />

Fresh<br />

Can3<br />

1,14<br />

Can/cream4<br />

Can/cream2<br />

Instant1<br />

-1,14<br />

HomeMade<br />

<strong>Procrustes</strong> principles<br />

set 2 tapioca<br />

set set<br />

3 4 5<br />

tapioca<br />

Standard set<br />

set 10<br />

9 8 tapioca<br />

tapioca<br />

set set 12 14 11 13 tapioca<br />

tapioca<br />

set set 7 6 tapioca<br />

set 1 tapioca<br />

Glass1


Expert data - attribute bitter<br />

GPA Group Average : dimension 1 versus 2<br />

1,14<br />

Instant1<br />

set 11 Froz/cream bitter<br />

Can5 Frozen1 set 12 bitter<br />

Can2<br />

Can4 set 5 bitter<br />

Can1<br />

-1,14 Can/cream1<br />

Fresh<br />

Can3<br />

1,14<br />

Can/cream4<br />

set 9 bitter<br />

Can/cream2<br />

set set 14 set bitter 13 3 bitter<br />

set 10 bitter<br />

HomeMade<br />

set 6 bitter set 4 bitter<br />

set 8 bitter<br />

set 1 bitter<br />

Standard<br />

set 7 bitter<br />

Glass1<br />

set 2 bitter<br />

-1,14<br />

<strong>Procrustes</strong> principles


Expert data - attribute color<br />

GPA Group Average : dimension 1 versus 2<br />

1,14<br />

Instant1<br />

-1,14 Can/cream1<br />

set 1 color<br />

Froz/cream<br />

Fresh<br />

Frozen1 Can5<br />

set 2 color<br />

Can2<br />

Can4<br />

set 8 color<br />

Can1<br />

set 5 color set 13 color<br />

Can3<br />

1,14<br />

Can/cream4<br />

Can/cream2<br />

HomeMade<br />

set 6 color<br />

set 14 color<br />

set 12 color<br />

set 10 color<br />

Standard set set 9 color 7 color<br />

-1,14<br />

<strong>Procrustes</strong> principles<br />

Glass1 set<br />

set<br />

4<br />

11<br />

color<br />

color<br />

set 3 color


Performance of individuals<br />

• for some attributes, there is excellent<br />

agreement<br />

• for other attributes there is much less<br />

agreement<br />

• the GPA results allow direct feedback to the<br />

tasters<br />

<strong>Procrustes</strong> principles


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data, different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program


Free Choice Profiling and GPA<br />

• N products are rated by K sets on m k attributes<br />

• each of the k sets uses different attributes<br />

• no descriptives possible<br />

<strong>Procrustes</strong> principles


Basic assumptions in FCP/GPA<br />

• the N products can be fitted in a K multidimensional<br />

spaces<br />

• the spatial structure of the K spaces can be<br />

defined in different ways<br />

<strong>Procrustes</strong> principles


Example 1: the dataset<br />

• experts from different countries rated the<br />

same products<br />

• 4 experts, 7 products, up to 6 attributes<br />

<strong>Procrustes</strong> principles


Four experts in space<br />

GPA Group Average : dimension 1 versus 2<br />

3,02<br />

set 6<br />

set 5<br />

set 7<br />

-3,02<br />

set 6<br />

set 2<br />

object set 7 5<br />

set 5<br />

object 3<br />

set object set set 7<br />

5 2 6<br />

set 5<br />

set 2 set 2<br />

set 7<br />

set 7<br />

set set 7object 5 6set<br />

2<br />

set 6<br />

object 1<br />

set 25<br />

set 6<br />

3,02<br />

-3,02<br />

set 5<br />

object 4<br />

set 2set<br />

7<br />

set 2<br />

set 6<br />

set 6<br />

object 7<br />

<strong>Procrustes</strong> principles


Permutation Results:<br />

Permutation test<br />

Total VAF in Real Data Set : 87,3 at 0 %<br />

Upper 10 % of the TVA in the permutated<br />

data Sets : 77,8<br />

Upper 5 % of the TVA in the permutated<br />

data Sets : 78,9<br />

<strong>Procrustes</strong> principles


Attributes of expert 2<br />

GPA Group Average : dimension 1 versus 2<br />

2,85<br />

-2,85<br />

object 5<br />

set 2 mealy<br />

object<br />

object<br />

set 2 2<br />

3<br />

bitter<br />

2,85<br />

set 2 fullness<br />

object 6<br />

-2,85<br />

object 4<br />

set 2 sour<br />

<strong>Procrustes</strong> principles<br />

object 7<br />

set 2 broth<br />

object 1


Attributes of expert 7<br />

GPA Group Average : dimension 1 versus 2<br />

2,85<br />

-2,85<br />

object 5<br />

set 7 sweet<br />

set<br />

object<br />

object<br />

7 broth<br />

2<br />

3<br />

set 7 creamy<br />

2,85<br />

-2,85<br />

object 4<br />

object 7<br />

set 7 fullness<br />

set 7 mealy<br />

<strong>Procrustes</strong> principles<br />

object 6<br />

object 1


Conclusions:<br />

• the data from the different experts can be<br />

summarized in a common group space<br />

• by comparing the attribute vectors of the<br />

different experts, we can identify the nature<br />

of the dimensions<br />

<strong>Procrustes</strong> principles


The data sets used in this presentation:<br />

• fcp.sts<br />

• expert75.sts<br />

• gower.sts<br />

• twoset.sts<br />

can be downloaded from our website<br />

<strong>Procrustes</strong> principles


• Introduction<br />

Today’s program<br />

• The <strong>Procrustes</strong> principles<br />

• Different data, different analysis<br />

• Some ‘sensory’ examples<br />

• Examples of FCP data<br />

• A hands-on demonstration<br />

• Discussion<br />

Program

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