Gene expression data analysis using R: How to make sense out of your RNA-Seq/microarray data

Course date: 08 July 2019 - 12 July 2019
Location: Erasmus MC OWR 22

Click here for details of programme
Click here to register for this course

Introduction & target audience
Five days hands-on computer course for biological and clinical researchers whose research involves experiments that generate gene expression data. The course focuses on microarray and next-generation sequencing gene expression data, but some concepts may be applicable to other types of genomics data. Most of the speakers (and therefore examples) have a biomedical background. Software packages used are freeware, including the statistical software R, Bioconductor, Cytoscape and web tools. The total number of participants is limited to 30.

Knowlegde of R required
For those of you who have no knowledge of R, it is required to work your way through the attached introduction in R. It is necessary to do so, because in this course we will not cover the basics of R but assume that you already have this basic knowledge.
Under abstracts/reviews in preparation of the course you will find a .zip file that contains: 
- instructions on how to install R
- exercises for R

Learning objectives
1. The participant has insight in the issues involved in good experimental design, including power to detect differential expression in microarray and next-generation sequencing data.
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.

Pre-requisites for participants
Participants need to know what a microarray 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? Affymetrix/ Illumina microarrays/ Agilent/ other: .....

Registration, deadline and admittance
The total number of participants is limited to 30.

The course is intensive, and covers the basic concepts and methods required for expression data 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.

Speakers and moderators (NB all speakers still have to be invited and have to confirm!)
• Judith Boer and Alex Hoogkamer, Department of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, Rotterdam
• Alex Hoogkamer, student Bioinformatics, HLO Leiden
• Karl Brand and Andrew Stubbs, Department of Bioinformatics, Erasmus MC, Rotterdam
• Henk Buermans, Leiden Genome Technology Center, LUMC
• Kristina Hettne, Marco Roos/Eelke van der Horst, Biosemantics Group, LUMC Leiden
• Maarten van Iterson, Department of Molecular Epidemiology, LUMC Leiden
• Jelle Goeman, Department of Biostatistics, Radboud University Nijmegen
• Renée de Menezes, Department of Epidemiology and Biostatistics, VUmc, Amsterdam
• Marcel Reinders, Information and Communication Theory Group, TU Delft
• Lodewyk Wessels, Bioinformatics and Statistics Group, Netherlands Cancer Institute, Amsterdam
• Guido Jenster, Department of Urology, Erasmus MC
• Guido Hooiveld and Peter van Baarlen, Nutrition, Metabolism & Genomics Group, Wageningen University
• Special course website: Sylvia de Does, Department of Bioinformatics, Erasmus MC


Course material from previous courses 

Here you can find the website with course material, also from previous courses:

Full participation in this course is 2,0 ECTS

Course organizers
Dr.Ir. Harmen van de Werken and Dr. Andrew Stubbs
Dr. Silvie Hansenova Manaskova and Dr. Frank van Vliet, Managing Director MolMed, 010-70 43518/ 06-5474 6408,

Related courses
MolMed (Erasmus MC) organizes annually several courses on R; the next one in May is open for registration.

Attendance fee
The subscription fee of non-commercial participants for the Course is €200 per day; 2 days €350.
Course tuition for non-commercial participants is € 750. Discounts are handled as followed:
•All participants from the Postgraduate School MolMed get a discount of 100 % 
•PhD students and research master students have 50% discount 
•Research master students who pay it themselves have 75% discount
We will send you an invoice (if applicable) after attending the course.
•If there is personal budget left, you need to use this in order to pay. Otherwise, IF you are a MolMed member you can participate for free.

0,3 ECTS per day;

General information
Financial regulation of the Postgraduate School MolMed

From January 1st, 2019 the following financial rules apply, but they may differ per course still. Look at the course fee of each course to be sure which discounts are really applied:

Non-commercial course, symposium or workshop fee: €200/day, €350/2days, €750/week.

• Participants of the postgraduate school MolMed: discount of 100%

• However, the Research Management course and the workshops Photoshop/Illustrator/Indesign have to be paid from the ‘personal budget’ of employees, MolMed members and PhD students included. So they will receive an invoice from us which you have to pay and which will be reimbursed by your Department. When you will pay from your personal budget you need to provide us your home address details for the invoice

• PhD students and Master’s students, regardless of institution: discount of 50%.

  • The course fees of research master’s students will be paid by their master program at rate of €100/ECTS. For not I&I master students: please inform your master program in advance whether they agree to pay.
  • Master’s students who are paying the fee from their private budget: discount of 75%. When you will pay from your personal budget you need to provide us your home address details for the invoice.
  • However, 2 courses in statistics are paid centrally by the Dept. of Research policy for all PhD students from Erasmus MC! These are R and the SPSS course. So for Erasmus MC PhD students, these courses are always free, provided you are officially registered as a PhD student.

There is one fee for the entire course. There is no reduction for partial participation.

Some courses have less course days: SPSS 3 days, Survival Analysis 2 days, Management 2 days, Presenting 1,5 days and also other may be shorter as indicated on the website.

Commercial participants, companies & sponsors are invited to inquire about commercial tuition fees and about sponsoring.

All invoices will be sent by email to the mail address that you filled in upon registration. If this address is not correct we use your Erasmus MC address.

Those who register for a course, symposium or workshop agree with these financial conditions.



Click here for details of programme
Click here to register for this course

Click here for the other items