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® Multivariate Data Analysis Version 4.0 Infometrix, Inc.

®

Multivariate Data Analysis

Version 4.0

Infometrix, Inc.

Pirouette® is licensed to you by Infometrix, Inc. You may only use this software in ac- cordance with the license agreement. You may use the software only on a single comput- er. You may not copy the software except for archive or backup purposes and you may not reverse engineer, decompile, or disassemble the software that comprises the Pirouette system.

Limited Warranty: Infometrix warrants that the software will perform substantially in accordance with the accompanying electronic documentation and optional written mate- rials for a period of 90 days from the date of receipt. Infometrix further warrants that any hardware accompanying the software will be free from defects in materials and work- manship under normal use and service for a period of one year from the date of receipt. Any implied warranties on the software and hardware are limited to 90 days and one year, respectively. Some states do not allow limitations on duration of an implied warranty, so the above limitation may not apply to you.

Customer Remedies: Infometrix’ entire liability and your exclusive remedy shall be, at Infometrix’ option, either (a) return of the price paid or (b) repair or replacement of the software or hardware that does not meet Infometrix’ Limited Warranty and which is re- turned to Infometrix with proof of purchase. This Limited Warranty is void if failure of the software or hardware has resulted from accident, abuse or misapplication. Any re- placement software will be warranted for the remainder of the original warranty period or 30 days, whichever is longer.

No Other Warranties: Infometrix disclaims all other warranties, either express or im- plied, including but not limited to implied warranties of merchantability and fitness for a particular purpose, with respect to the software, any accompanying hardware, and the ac- companying written materials. This limited warranty gives you specific legal rights, but you may have others, which will vary from state to state.

No Liability for Consequential Damages: In no event shall Infometrix or its suppliers be liable for any damages whatsoever (including, without limitation, damages for loss of business profits, business interruption, loss of business information, or other pecuniary loss) arising out of the use or inability to use this Infometrix product, even if Infometrix has been advised of the possibility of such damages. Because some states do not allow the exclusion or limitation of liability for consequential or incidental damages, the above limitation may not apply to you.

Infometrix and Pirouette are registered trademarks, and InStep and LineUp are trademarks of Infometrix, Inc. Acrobat, FrameMaker, Adobe, Matlab, Lotus and Lotus 1–2–3, Excel, Microsoft, Windows NT, Windows 2000, Windows XP, and Windows 98, GRAMS, Lab Calc, Spectra Calc, OPUS, PIONIR, EZChrom, VStation, ChemStation and Millennium are trademarks of their respective owners.

Copyright © 1985–2008 by Infometrix, Inc. All rights reserved. Infometrix, Inc., 10634 E. Riverside Dr., Suite 250, Bothell, WA 98011 Phone: (425) 402-1450, FAX: (425) 402-1040, Information: info@infometrix.com, Support: support@infometrix.com World Wide Web: http://www.infometrix.com/

Preface

A lthough the growth of computing technology has enabled users to collect ever in- creasing amounts of data, software in many respects, has not kept pace with how

we use our hardware. In a day an analytical instrument coupled to a reasonably fast computer can collect data on many samples, each with hundreds of variables. The soft- ware bundled with most instruments is not designed to extract meaningful information efficiently from such large data sets. Instead, the emphasis is on spewing (compiling and printing tables) and storing (archiving them for later retrieval). Moreover, although the data may be multivariate, most data analysis software treats it as a succession of non-cor- related, univariate measures.

Today’s technology demands a better approach: one that acknowledges not only the non- specific and multivariate nature of most instrumented data but also common bottlenecks in the data analysis process:

a plethora of algorithms which can distract or even confuse the user

the lack of a standard file format to ease the blending of data from several instrument sources

non-intuitive and non-graphical software interfaces which steepen an already chal- lenging learning curve

the absence of a mechanism to organize all computations performed on a data set into a single file

Welcome to Pirouette

The Windows version of Pirouette was developed to address all of the problems men- tioned above while also taking advantage of the stability and standardization of the cur- rent 32-bit Windows operating systems which permit virtually unlimited file size and true multitasking/multithreading.

One key strength of Pirouette is the complete integration of graphics. Typically, the result of an analysis is a graphic or group of graphics. These range from 2D plots and line plots to dendrograms and rotatable 3D plots. Multiple plots in different windows are automat- ically linked, where appropriate, so that when two or more graphics are on screen, sam- ples highlighted in one display are also highlighted in the others. For example, samples highlighted in a principal component scores plot will also be highlighted in a dendro- gram.

Performing analyses rapidly and easily is important; however, the saving and re-using the results of these analyses as models is equally important. With Pirouette, working with model files is as easy as working with any other file. Any model created within Pirouette

Preface

can be saved and re-loaded later; predictions on new samples do not require rebuilding the model.

We have audited the way the majority of our users work and found that a stand-alone manual, regardless of its quality, is consulted infrequently. We decided, therefore, to sup- ply the documentation as an electronic help file. Complete information is at your elec- tronic fingertip in the form of a portable document format, complete with hyperlinked text. To obtain a hardcopy of any portion of this user guide, simply print from the Acrobat Reader, shipped with the software.

We believe Pirouette to be the most powerful and yet easy to use statistical processing and display program available. The routines included in this version are broadly applica- ble and often encountered in the chemometric literature. The graphical representations of the data and the interactive windowing environment are unique. As we continue to refine the software interface and enhance the statistical features of Pirouette, we look forward to your comments.

Happy computing and thanks for selecting Pirouette!

Structure of the Documentation

The document you are reading is organized with the goal of training you in multivariate analysis, regardless of your chemometrics background or level of experience in window- ing interfaces. The basic thrust of each major section is listed below. Several chapters re- fer to data sets included with Pirouette. If you follow along with our examples, you will better understand both the points made in the chapter and how to work with Pirouette to analyze your own data sets.

PART I INTRODUCTION TO PIROUETTE

This section briefly introduces the Pirouette environment, discusses the software instal- lation, and explains how to run a Pirouette analysis and build both classification and re- gression models for future use.

Chapter 1, Quick Start This introductory chapter contains everything you need to get started with Pirouette. Basic features of the Pirouette environment are described, including data input, running algorithms and viewing data and results.

Chapter 2, Pattern Recognition Tutorial This chapter walks through the analysis of a classification data set to introduce the Pirouette environment and explain some of the thought processes behind multivariate analysis.

Chapter 3, Regression Tutorial This chapter walks through a detailed analysis of a re- gression data set to introduce the Pirouette environment and multivariate analy- sis. It can augment or replace the instruction given in Chapter 2.

PART II GUIDE TO MULTIVARIATE ANALYSIS

Part II explains how to perform a multivariate analysis with Pirouette while also serving as a textbook on the multivariate methods themselves.

Chapter 4, Preparing for Analysis This chapter discusses how to prepare data for analysis. Details of transforms and preprocessing options are included.

Preface

Chapter 5, Exploratory Analysis This chapter explains how to run an exploratory data analysis. The two exploratory algorithms contained in Pirouette, Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA), are explained in detail, along with a discussion of how to manipulate and interpret their graph- ical results.

Chapter 6, Classification Methods This chapter explains how to build a classification model and use it to classify unknown samples. Pirouette’s two classification al- gorithms—K-Nearest Neighbor (KNN) and Soft Independent Modeling of Class Analogy (SIMCA)—are discussed in detail with an emphasis on how to interpret the results of each.

Chapter 7, Regression Methods This chapter explains how to build a multivariate re- gression model and use it to predict continuous properties for unknown samples. Pirouette’s two factor-based regression algorithms—Partial Least Squares (PLS) and Principal Component Regression (PCR)—are discussed jointly in de- tail. The results of the two algorithms are interpreted separately and compared. Classical Least Squares (CLS) is also described and contrasted with PLS and PCR.

Chapter 8, Mixture Analysis This chapter describes methods used to resolve mixtures into their underlying components. Multivariate Curve Resolution can be used to deconvolve fused chromatographic peaks and can apportion mixtures into their source compositions.

Chapter 9, Examples This chapter contains a series of application vignettes which can be a starting point for your own specific work. We have built this chapter as an overview of different data sets; many are supplied with Pirouette so that you can experiment with the data yourself.

PART III SOFTWARE REFERENCE

Part III is a guide to the Pirouette graphical interface, giving helpful hints so that you can exploit its full power. This section also serves as a technical reference for the various but- tons, menu options and features unique to the Pirouette environment.

Chapter 10, The Pirouette Interface This chapter explains how Pirouette’s tools, cur- sors and buttons are used to manipulate and interact with tabular and graphical displays. In addition, we discuss linking of results shown in different screen win- dows and how to create data subsets from the graphic display.

Chapter 11, Object Management This chapter explains how to use a central compo- nent of Pirouette, the Object Manager, for accessing data subsets and computed results.

Chapter 12, Charts This chapter describes the various types of graphs available in Pir- ouette, along with explanations of how to navigate and manipulate each.

Chapter 13, Tables This chapter describes how to hand enter and modify data within the spreadsheet. Also included are explanations of how to create subsets from ta- bles and the navigation, sorting and editing tools.

Chapter 14, Data Input This chapter discusses reading and merging existing files to form a project-oriented Pirouette file.

Chapter 15, Output of Results This chapter explains how to print and save Pirouette objects and files, including how to save Pirouette model files for use in future pre- dictions.

Preface

Chapter 16, Pirouette Reference This chapter describes all Pirouette menu options and dialogs.

PART IV APPENDICES

A series of subjects are addressed in appendices, including troubleshooting suggestions.

Chapter 17, An Introduction to Matrix Math This chapter gives a background in the matrix mathematics underlying all of Pirouette’s multivariate algorithms. In addi- tion, it describes nomenclature used in presenting equations.

Chapter 18, Tips and Troubleshooting This chapter details the error messages in Pir- ouette and tips on what you may be able to do when confronted with an error.

PIROUETTE RELEASE NOTES

A “Release Notes” document accompanies the materials that comprise Pirouette. Peruse

this file to learn about new features and enhancements in recent versions as well as known problems.

ACKNOWLEDGMENTS

The creation of Pirouette was a team effort which traces its origins back to the late 1970s and early 1980s when the desire for such a product was strong, but the tools to create it were weak. The team included a number of special individuals in government, academia and industry who supplied comments and provided down–to–earth applications. We par- ticularly wish to acknowledge the suggestions and input of the following individuals:

Fred Fry

Rick Murray

David Haaland

Randy Pell

Arnd Heiden

Mary Beth Seasholtz

Russell Kaufman

Takehiro Yamaji

Vanessa Kinton

Major contributors at Infometrix are noted below.

Development:

Marlana Blackburn

Scott Ramos

Jay Matchett

Brian Rohrback

Support:

Paul Bailey

Duane Storkel

It is also appropriate to mention those who contributed significantly to prior versions of

Pirouette and related Infometrix products. The efforts of Barry Neuhaus, Susannah Bloch, Gerald Erickson, Meeji Ko, Carol Li, Stacey Miller, David Summers, Tom Wanne, Dean Webster and Joseph Yacker all helped lay the groundwork for this soft- ware.

Preface

We would like to acknowledge the following individuals who contributed to the transla- tions of the user interface.

French:

Jean-François Antinelli

Analytics Consulting, Nice, France

German:

Arnd Heiden and Carlos Gil

Gerstel GmbH & Col. KG, Mulheim an der Ruhr, Germany

Italian:

Giuliana Drava

Dept of Pharmaceutical and Food Chemistry, University of Genova, Italy

Japanese:

Masato Nakai and Takehiro Yamaji

GL Sciences, Tokyo, Japan

Portuguese:

Scott Ramos

Infometrix, Bothell, WA

Spanish:

Scott Ramos, Vanessa Kinton and Rodolfo Romañach

Infometrix, Bothell, WA; Washington, DC; and Universidad de Puerto Rico, Mayagüez, Puerto Rico

This user guide was produced using Adobe's FrameMaker publishing package, and con- verted to a portable document format for online viewing.

Preface

Contents

Part I. Introduction to Pirouette

Chapter 1

Quick Start

Pirouette Briefly

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1-1

. Running Algorithms

Data Input

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. 1-2

. 1-2

Viewing

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1-3

The Object Manager

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1-4

. Saving Data and Models

Saving Images

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. 1-5

. 1-5

Pirouette Help

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. 1-6

Technical Support

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1-6

Chapter 2

Pattern Recognition Tutorial

 

The Basics

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. 2-1

Define the Problem

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2-1

Open the File

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Examine the

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. 2-4

Exploratory Analysis.

. Running Exploratory Algorithms

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. 2-7

2-7

Data Interpretation .

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. 2-10

Modeling and Model Validation

 

2-19

KNN Modeling

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. 2-19

Review

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. 2-24

References

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. 2-24

Chapter 3

Regression Tutorial

The Basics

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. 3-1

Define the Problem

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3-1

Organize the Data

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. 3-2

Read the File

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. 3-2

Examine the

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. 3-5

Exploratory Data Analysis

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. 3-7

. Running the Exploration

Set Up

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3-8

3-9

Data Interpretation .

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. 3-11

Contents

 

The Next Step: Calibration .

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3-17

Calibration and Model Validation

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3-17

Set Up

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3-18

Calibration with PCR and PLS

 

3-18

Data Interpretation

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3-20

Saving the Model

Prediction of Unknowns

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3-30

3-32

Review

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3-36

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3-36

Part II. Guide to Multivariate Analysis

 

Chapter 4

Preparing for Analysis

Overview

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4-1

Defining

the Problem

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4-3

Organizing the Data

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4-4

Assembling the Pieces

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4-4

Training Set Structure

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4-5

Checking Data Validity

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4-5

Visualizing the Data.

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4-6