27411 Biological Data analysis and chemometrics (Spring 2012)

Updated: 19/03 2012

Course description:

For a detailed course description please take a look at the "Course database" (in English, in Danish).
The course will be held in english.

Provisional Lecture plan:

#	Date	Lecturer	Topic(s)	Litterature	Hand-out's and useful links	Exercise
1	30/01	PBB/JCF	Introduction JCF, PBBexample, QSARposterPBB)	Lattin, ch.1 and 2	Esbensen, p. 115-180	Intro Exercise
2	06/02	PPB	Multivariate linear regression (Slidehandouts)	Lattin, ch. 3	MLR in UNSCRAMBLER	MLR Exercise MLR Exercise 3
3	13/02	JCF	Principal Component analysis 2010: Slides in Campusnet (Slidehandouts2009)	Esbensen (p. 19-113)		PCA Exercise Data: vinout.txt, fisherout.xls
4	20/02	PPB	Principal Component Regression (Slidehandouts)	Lattin ch. 4, Esbensen (p.115-136,155-170)		Exercise
5	27/02	JCF	Classification I - "SIMCA" (Slidehandouts)	Read Unscrambler help		Exercise
6	05/03	PPB	Partial Least Squares Regression (PLShandouts)(PLShandouts2)	Esbensen (p. 137-154, 171-180)		Exercise PLS Exercise 2
7	12/03	PBB	Classification II - "classical" (Slidehandouts)	Lattin, ch. 12 (sec. 12.1 - 12.8) Help pages in Unscrambler.	Hand calculation exercise(and solution)	Exercise
8	19/03	PPB	Ridge Regression (PPB)	Hastie et. al. (p. 59-63)		Exercise
9	26/03	JCF	Correspondence Analysis (JCF)	Recommended readings: 1, 2, 3. Supplementary readings: NTSYS (sec. 9.14 - 9.24)		Exercise Data: EU.txt, Lebart.txt
10	16/04	JCF	Cluster Analysis (JCF)	Lattin, p. 264-288 Handouts p. 7-13		Exercise (.pdf) Data: vin.txt, sm.txt Datafile vin explanation (.pdf)
11	23/04	JCF	Non metric Scaling
12	30/04	PBB/JCF	Guest Lectures
13	07/05	JCF PBB	Overview/summary lectures Questions Course evaluation

Student presentations:

All students are divided into groups of 2-3 people. Each group are supposed to present one topic/exercise each. These
presentations can be seen as direct rehearsals of the final oral exam, that are thought to be of the following structure:

5 minutes overall description of the method
10 minutes discussion about the data analysis results from the exercise

The topic of each of the presentations is lister here:

Topic no	Presentation date	Topic
1	13/02	Multivariate linear regression
2	20/02	Principal Component analysis
3	21/02	Principal Component Regression
4	05/03	Classification I, Simca
5	12/03	Partial Least Square Regression
6	19/03	Classification II
7	26/03	Ridge Regression
8	16/04	Correspondence analysis
9	23/04	Cluster analysis
10	30/04	(Non Metric Scaling)

The groups are:

Topic	Groups
1	Anne+Casper
2	Rasmus + Rasmus
3	Lene + Jacob
4	Damian + Anders
5	Jesper + Stefan
6	Anne + Casper
7	Sune
8
9
10

General information:

Time:
Mondays 13:00 - 17:00.

Location:
Lectures and exercises: Building 210, Room 052.

Lecturer(s):

JCF: Professor Jens C. Frisvad (CMB)
Building 221, Office 204
Tel.: +45 4525 2626
Email: jcf(a)bio.dtu.dk
PPB: Professor Per M. B. Brockhoff (IMM)
Building 321, Office 032
Tel.: +45 4525 3365
Email: pbb(a)imm.dtu.dk

Litterature:

James Lattin, J. Douglas Carrol and Paul E. Green, "Analyzing Multivariate Data". (Errata)
(can be bought in the book store in Building 101)
Additional material will be handed out during the semester.

Final examination:

The final examination will be oral.

Usefull links:

Software:

NT-SYS (Numerical taxonomy and multivariate analysis system).
Version 2.10 (F. James Rohlf). Exeter Software, 100 North Country Road, Building B, Setauket, New York 11733, USA
UNSCRAMBLER.
Version 8 (CAMO A/S, Box 1405 Vika, N-0115 Oslo, Norge, E-mail: Camo@Camo.no)

In addition other programs are available: SAS, R, and Matlab.