This is a genomics data analysis support site for VU/VUmc researchers.  Consult
We are happy to help VU/VUmc researchers with genomics data analysis questions. Please first complete the consult form available here. Priority will be given to in-house produced genomics data.


VU/VUmc genomics data analysis meeting (updated weekly)

This meeting is organized weekly on Fridays 10.30h-11.00h and centered around one discussion theme, which is hopefully of general interest. It discusses analysis issues for aCGH and/or gene expression data. The meeting is followed by consult on individual basis. Please send a mail to mark.vdwiel[at]vumc.nl  when you have a topic of interest or when you want to consult the statisticians/bioinformaticians after the meeting.

2006
13/10: Normalization of aCGH data. 
20/10: STAC, finding focal positions on DNA profiles. 
27/10: Agilent gene expression arrays: single channel, dual channel, reference material or not...? What data do we have, what experiments do we need?
03/11: CGHregions: data-driven construction of clone/oligo regions, LOCATION CCA!!!
10/11: aCGH, detection of associated chromosomal regions
17/11: aCGH/expression integration, Speakers: Marcel Kool and Jan Koster (AMC), Location: PK 7Z163, De Peel
25/11: aCGH, clustering of arrayCGH with WECCA (CCA1.06)
01/12: NO GDA meeting
08/12: QC and limma on gene expression arrays, Location: PK 7Z163, De Peel
15/12: Expression: DIGMAP, software to link gene expression with chromosomal position,
(Blue extension on top of policlinic)
22/12: Data analysis flow for aCGH data. Location: PK 7Z163, De Peel

2007
12/01: CGHtest: statistical testing for arrayCGH data. Location: CCA 1.06.
19/01: How to find the most relevant features (genes/clones) which are different between clusters and how to define their 'confidence'?
26/01: Do's and don'ts of microarray data analysis. Discussion of review paper: Dupuy & Simon (2007) "Critical Review of Published Microarray Studies for Cancer Outcome and Guidelines on Statistical Analysis and Reporting" J Natl Cancer Inst;99: 147 – 57.
Location: CCA 1.06.
01/02: Consult hour. Location: CCA 1.06
08/02: What do we mean by "Integration of aCGH and gene expression data"? Discussion. Location: CCA 1.06
17/02: Fuzzy clustering of aCGH data. Presentation by Sjoerd Vosse (master's thesis). Location: CCA 1.06
25/02: No meeting
02/03: No meeting
09/03: No meeting
16/03: Discussion of analysis of Serge Smeets' 3 group (HPV, p53 mutated/non mutated) aCGH data.
Application of CGHtest R-script.
23/03: Critical assessment of aCGH normalization: problematic profiles. Contributions from Gerard Schaafsma and Tineke.
30/03: Design of experiments for two-colour experiments. Discussion of R-software smida by Wessel illustrated on a project from Thijs van Boxtel (Institute for Environmental Research, VU)
06/04: No meeting
13/04: Discussion on testing for differential expression using GO nodes, with contribution from Ben Nota (VU, Ecology)
20/04: Quality Control for Agilent gene expression arrays. Demonstration of R-script for assessing the quality of your arrays.
27/04: No meeting
04/05: No GDA meeting (MC-gard!)
11/05: Demonstration of  aCGH database by Floris Sicking (LIACS), Erwin Bakker (LIACS), Sjoerd and Mark, 10.30h-11.45!!!  CCA1.06.
18/05: No meeting
25/05: Discussion: Internal and external validation of array results; p-values revisited. CCA 1.06.
01/06: Discussion: Cellularity, ploidy and DNA index, improving calls for aCGH data. CCA 1.06.
08/06: Presentation by José Fereirra (KEB): Benjamini-Hochberg multiple testing corrections for discrete data. CCA 1.06
15/06: No meeting
22/06: No meeting
29/06: Discussion of Genomics Data Analysis consult form available from VUmc pathology site.
06/07 - 10/08: No meetings
13/08: MONDAY. Web-meeting: Soheil Shams, BioDiscovery (USA) presents the results of their software for aCGH data analysis on our data.  CCA 1.06, 16.00h.
17/08: No meeting
24/08: No meeting, CTMM symposium
27/08: MONDAY. Johannes Peham (Cranfield / VUmc) presents data analysis aspects of his internship: LIMMA analysis on mouse expression data. CCA 1.06, 10.30h.
31/08: Classification of segmented aCGH data (colon) by four algorithms: a comparative study. Presented by Gerard Schaafsma. 
07/09: No meeting
14/09: No meeting
21/09: No meeting
24/09: MONDAY. Andreas Glatz (Cranfield / VU) presents a new classification algorithm for called aCGH data
28/09: Jan Oosting (LUmc):  the use of genotype information and flow-sorting to improve copy number calculations in high resolution SNP arrays
05/10: No meeting (Computer practicum Microarray course)
12/10: Pierre Neuvial (Institut Curie): CAPweb ("A web-based platform for CGH-array management and analysis"; http://bioinfo-out.curie.fr/CAPweb/), with a focus on methodological issues: normalisation (of CGH and SNP arrays) and correlation between DNA copy number and expression levels
19/10: No meeting (CCA/Vici symposium)
26/10: Single channel analysis of dual channel expression arrays, discussion
02/11: Feedback discussion on CGHcall
16/11: Bauke Ylstra: FFPE samples on Affymetrix; includes VUMC colon (CAIRO) gastric and H&N samples 
30/11: Wouter Peyrot: Use of complete remission prognosis for forecasting survival, applied to a cohort of leukemia patients
14/12: Joost Oudejans: discussion on the following Genomic signatures to guide the use of chemotherapeutics

2008
18/01: How large a data set is needed to to develop a classifier for microarray data? Discussion by Wessel van Wieringen
25/01: MPS; moving on to the 3rd generation sequencing. Discussion by Bauke Ylstra


Software
We develop software for the analysis and integration of array CGH and gene expression data. An overview, including a list of useful external software, is available here.

Our arrayCGH data analysis flow (PowerPoint poster)

Links
VUmc Micro-array core facility
VUmc Cancer Center
Statistics for life sciences Amsterdam