Gene expression data analysis using R:
How to make sense out of your RNA-Seq/microarray data
June 22-26, 2015
Organised by MolMed
15th edition, Erasmus MC
vs 150615
Course organizers and website
Program: Dr. Judith Boer
Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, j.m.boer@erasmusmc.nl
Coordination: Dr. Frank van Vliet
MolMed, 010-70 43518/ 06-5474 6408, f.vanvliet@erasmusmc.nl
Website: www.molmed.nl
Course website: http://molmed-expression.erasmusmc.nl/
Speakers and moderators
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Judith Boer and Alex Hoogkamer, Department of Pediatric Oncology, Erasmus MC-Sophia
Children's Hospital, Rotterdam
Henk Buermans, Leiden Genome Technology Center, LUMC
Marcel Reinders and Erdogan Taskesen, Information and Communication Theory Group,
TU Delft
Renée de Menezes, Department of Epidemiology and Biostatistics, VUmc, Amsterdam
Lodewyk Wessels and Jelle ten Hoeve, Bioinformatics and Statistics Group, Netherlands
Cancer Institute, Amsterdam
Jelle Goeman, Department of Biostatistics, Radboud University Nijmegen
Maarten van Iterson, Department of Molecular Epidemiology, LUMC Leiden
Guido Jenster, Department of Urology, Erasmus MC
Job van Riet, Cancer Computional Biology Center and Department of Urology, Erasmus MC
Andrew Stubbs, Department of Bioinformatics, Erasmus MC, Rotterdam
Kristina Hettne and Eelke van der Horst, Biosemantics Group, LUMC Leiden
Peter van Baarlen, Nutrition, Metabolism & Genomics Group, Wageningen University
Course website: Sylvia de Does, Department of Bioinformatics, Erasmus MC
Location: Erasmus MC, Computerroom 22, Onderwijscentrum.
Target group
The course is tailored for biological and clinical researchers whose research involves
experiments that generate gene expression data by using RNA sequencing or microarrays.
The course focuses mostly on the analysis of expression data, and explains general concepts
such as experimental design, normalization, testing and interpretation. We do not explain the
technologies themselves and we do not cover the mapping of sequence reads. Dedicated
courses for next-generation sequencing and RNA-seq covering these topics are available (see
http://biosb.nl). Some concepts may be applicable to other types of genomics data. Most of
the speakers (and therefore examples) have a biomedical background.
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Pre-requisites for participants
Participants need to know what a microarray or RNA sequencing experiment is, and have
their own expression profiling data. They have preferably followed an introduction to R
course; alternatively they have practiced the "Getting started in R" practical prior to the
course. Basic statistical concepts including mean, variance, standard deviation, probability
distributions, t-test, p-value, correlation, and linear regression are assumed known. These are
typically seen during basic statistics courses. Please fill in the online registration form
(in the free text box at the bottom of the form):
 do you have basis R knowledge (yes/no); if yes, please indicate how you
acquired this knowledge: basic R course/ other…;
 do you have gene expression data to analyse yes/no, if yes: which platform?
Microarrays: Affymetrix / Illumina / Agilent / other: .....
RNA sequencing: tag / transcriptome / other: .....
Format
The course is intensive, and covers the basic concepts and methods required for expression
analysis. Presentations are followed by hands-on computer sessions to directly apply and get
more insight in the analysis methods. One afternoon is dedicated to the analysis of a new
data set, allowing the students to refresh and extend their analysis skill. After the course, the
presentations, practicals and test data will remain available for future reference. Software
packages used are freeware, including the statistical software R, Bioconductor, Cytoscape and
web tools.
Learning objectives
1. The participant has insight in the issues involved in good experimental design of
microarray and next-generation sequencing experiments.
2. The participant knows and can perform analysis steps in expression data analysis, visually
present and judge the results for:
 quality control and preprocessing,
 finding differentially expressed genes,
 cluster analysis,
 classification analysis,
 pathway testing.
3. The participant has insight in the different algorithms and options available to perform an
analysis, and can make an informed choice.
4. The participant knows the pitfalls of existing analyses and is able to critically judge the
statistical analysis of expression data performed by others.
Registration, deadline, admittance, sponsored places & related courses
The total number of participants is limited to 40. Deadline for registration is four weeks in
advance, on Monday 25 May, 9 a.m. When more than 40 students register before this
deadline, the organisers will make a selection and admit the students with own data
and experience in R. Please note that to this aim you must fill in the online registration
form:
 do you have basis R knowledge (yes/no); if yes, please indicate how you acquired this
knowledge: basic R course/ other…;
 do you have gene expression data to analyse yes/no, if yes: which platform? Microarrays:
Affymetrix / Illumina / Agilent / other: ..... RNA seq: tag / transcriptome / other: .....
LUMC organizes a basic course in R from 9-10 June 2015; www.boerhaavenet.nl. MolMed
(Erasmus MC) organizes a basic course on R from 26-29 May 2015; www.molmed.nl.
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Programme
Day 1
Room
Monday June 22: Design and Preprocessing
Rooms: computer room 22 (Onderwijscentrum)
Moderator : Judith Boer
9:15
9:45
10:00
10:45
11:00
12:00
13:00
13:45
14:00
14:15
17:00
Welcome coffee and registration
Short introduction to data sets and tools
Introduction to microarray and RNA-seq
technology
Coffee
Experimental design: Think before you start
Lunch (in room Ae-406)
Normalization
Introduction to R and Bioconductor
Coffee
Practical: Normalization and quality control in
R: platform comparison data Affymetrix,
Agilent, Illumina arrays, Solexa (RNA-Seq)
End day 1
Judith Boer
Henk Buermans
Judith Boer
Judith Boer
Judith Boer
Judith Boer, Alex Hoogkamer,
Andrew Stubbs
Day 2 Room Tuesday June 23: Gene testing and Clustering
Room: Computer room 22 (OWR)
Moderator: Renée de Menezes
8:45
9:00
10:00
10:15
11:15
12:30
13:30
14:45
15:00
17:00
Welcome coffee
Hierarchical and K-means clustering
Coffee
Cluster validation and principal component
analysis
Practical: Clustering using R
Lunch (in room Ae-406)
Finding differentially expressed genes
Coffee
Practical: Finding differentially expressed
genes in R using limma / edgeR
Marcel Reinders
Marcel Reinders
Marcel Reinders with assistance
Renée de Menezes
Renée de Menezes, Judith Boer,
Alex Hoogkamer
End day 2
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Day
3
Room Wednesday June 24: Classification and Gene set testing
Room: Computer room 22 (OWR)
Moderator: Lodewyk Wessels
8:45
9:00
10:30
10:45
12:30
13:30
14:30
14:45
17:00
Day
4
Welcome coffee
Classification and PAM
Coffee
Practical: Classification using PAM
Lunch (in room Ae-406)
Testing groups of genes
Coffee
Practical: Testing groups of genes
End day 3
Lodewyk Wessels
Lodewyk Wessels, Jelle ten Hoeve
Jelle Goeman
Jelle Goeman with assistance
Room Thursday June 25: Practical Issues and Practice
Room: Computer room 22 (OWR)
Moderator: Judith Boer
8:45
9:00
9:45
10:30
10:45
11:15
Welcome coffee
Gene annotation
Practical: Gene annotation
Coffee
Batch effects
Practical: Batch effects
12:00
13:00
Lunch (in room Ae-406)
Gene expression profiling: the cancer
transcriptome
Coffee
Assignment: Data analysis of ALL samples
14:00
14:15
15:45
16:00
Coffee
Assignment: Data analysis of ALL samples,
continued
End day 4
17:00
Day
5
Room
Maarten van Iterson
Maarten van Iterson, Judith Boer
Judith Boer, Maarten van Iterson
Judith Boer, Maarten van Iterson,
Alex Hoogkamer
Guido Jenster
Judith Boer, Andrew Stubbs, Alex
Hoogkamer, Job van Riet
Judith Boer, Andrew Stubbs, Alex
Hoogkamer, Job van Riet
Friday June 26: Databases and Pathways
Room: Computer room 22 (OWR)
Moderator: Andrew Stubbs
8:45
9:00
9:45
10:30
10:45
12:15
13:15
15:30
15:45
17:00
Welcome coffee
Databases and pathway analysis
Interpretation of gene lists
Coffee (in room Ae-406)
Practical: Practical: Interpretation of gene
lists with the Anni Web Service and DAVID;
Databases and pathway analysis
Lunch
Presentation Cytoscape
Coffee
Practical Cytoscape
End day 5: hand in evaluation form & badge!
Andrew Stubbs
Kristina Hettne, Eelke van der
Horst
Kristina Hettne, Eelke van der
Horst
Peter van Baarlen
Peter van Baarlen
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Attendance fees
Course tuition for non-commercial participants is € 700. Discounts are handled as followed:
 Participants from the postgraduate school MolMed get a discount of 100% (tuition =
€0).
 PhD students and Master’s students, regardless of institution, get a discount of 50%
(tuition = €350).
The course is considered an entirety, and participants are encouraged to attend all parts of
the course. No discounts are given for participants who chose not to participate in a portion of
the course.
If these financial requirements pose a problem, please contact Frank van Vliet, managing director of the Erasmus
Postgraduate School Mol Med, at: f.vanvliet@erasmusmc.nl.
Invoices
Fees should only be paid after receipt of an INVOICE. Shortly after your registration you will
receive the INVOICE by mail. Payment should be transferred to account: 43.47.01.408 /
Erasmus MC, (IBAN code bank: NL86ANBA0434701408; SWIFT code bank: ABNANL2A), with
the invoice number noted. Late registrations may also pay in cash upon arrival.
Cancellations
Cancellation is possible up to one week before the start of the Course. Later
cancellation will not be accepted, but you are allowed to send a substitute.
Commercial participants & sponsors
Companies are invited to inquire about commercial participant tuition fees and about
sponsoring.
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