DNA Microarray Analysis - CBS · 2011. 1. 2. · DNA Microarray Analysis Course #27612 3-21 January 2011 DTU Center for Biological Sequence analysis (CBS) søndag den 2. januar 2011

DNA Microarray AnalysisCourse #27612

3-21 January 2011

DTU

Center for Biological Sequence analysis (CBS)

søndag den 2. januar 2011

Carsten FriisAssistant professorChemical Engineer and PhD from DTUWorked with bioinformatics since 1997 and microarray data since 2000

Teaching on this course: R and Exercises in Statistics.

of the course

Teachers


Agnieszka JunkerGraduate Engineer and PhD in Bioinformatics from DTUWorked with bioinformatics and microarray data since 2000

Teaching on this course: Dimension reduction, several exercises & assistant course coordinator.

of the course

Teachers


Nils Weinhold & Tune PersPhD studentsSpecializes in Human Disease Genetics

Teaching on this course: Genome Wide Association

of the course

Teachers

Nils

Tune


5

of the course

Additional Teachers

Hanne Jarmer


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman

Simon Rasmussen


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman

Simon Rasmussen

Ramneek Gupta


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman

Simon Rasmussen

Ramneek Gupta

Kirstine Belling


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman

Simon Rasmussen

Ramneek Gupta

Kirstine Belling

Agata Wesolowska


5

of the course

Additional Teachers

Hanne Jarmer

Aron C. Eklund

Chris Workman

Simon Rasmussen

Ramneek Gupta

Kirstine Belling

Ulrik Plate

Agata Wesolowska


H. Bjørn Nielsen Associate professorMC in Biology (KU), PhD from DTUWorked with microarray data since 1999

Teaching on this course:, Preprocessing, Statistics, Project work and Course organizer

of the course

Teachers


The course has 36 students signed up

2 Bachelor students (2 bioteknologi)

22 Master students (11 System Biology, 11 bioteknologi)

10 PhD students

2 guest students

the students

Who are you


･ Account for the individual steps in a general microarray analysis･ Explain the overall theoretical principles behind the individual steps in the

analysis･ Account for the preconditions and assumptions in the individual steps of

the analysis･ Independently apply a basal microarray analysis･ Read into and manipulate simple data structures in the statistical

computing environment R･ Formulate problem formulations that may be answered by microarray

analysis･ Answer the problem formulated by the students･ Collaborate in a group about the project work

for the course

Learning Objectives (L.O.)


for the course

Learning Objectives (L.O.)

That the student learn

A) To apply the methods for microarray analysis on real data

C) To manipulate simple data structures in the statistical computing environment R

B) To formulate interesting hypotheses that can be addressed by microarray data analysis


of the course

Content

Tree main tracksA) Lectures, discussions and exercises

on microarray analysis

B) Lectures and exercises on R

C) Problem formulation and project


Project Period

time schedule

The Course Tracks

Intro The Pipeline Advanced Analysis

Project Intro ProblemFormulation Project

PosterSessionR Learning by doing

Array exercises

12th of January 21th of January3th of January


Track A: The DNA Array Analysis Pipeline

Sample PreparationHybridization

Design Arrayor bye a

standard array

Experimental Design

Statistical AnalysisFit to Model (time series)

Expression IndexCalculation

Advanced Data AnalysisClustering PCA Gene Annotation Analysis Promoter Analysis

Classification Meta analysis Survival analysis Regulatory Network

ComparableGene Expression Data

Normalization

Image analysis

Question/hypothesis

NGS data

Mapping


problem formulation

Track C

Group formation

Problem formulation (Finalized, Wednesday week 2)

Projects (Initialized Wednesday week 2)

Poster session (21th of January, exam)


Course web page

• Course program• Lecture Slides• Exercises• And more

www.cbs.dtu.dk/chipcourse


Documents

DNA Microarray Analysis - CBS · 2011. 1. 2. · DNA Microarray Analysis Course #27612 3-21 January 2011 DTU Center for Biological Sequence analysis (CBS) søndag den 2. januar 2011