VUmc array CGH data analysis flow

VUmc array CGH data analysis flow
Database
Imaged files
BlueFuse,
Agilent
LIACS
•Queries (subsets)
•Raw log-ratios
•Clone lists
•Flags
•Stanford format
•Quality plots
•Storage
CGHcall
CGHregions
Bioinf (2007)
Cancer Inf (2007)
•Regions from calls;
minimal information loss
•Pre-processing: filtering,
imputation,normalization,
segmentation
•More robust and powerful
statistics
•Objective calling
CGHtest
Clustering
Expr-aCGH
CGHMultiArray
WECCA
ACE-it
Bioinf (2005)
Biostat (2007)
•Statistical tests: 2- and Ksample, multiple comp.
•Clustering of aCGH samples
•Alignment DNA-RNA elements
•Several metrics and linkages
•Test for differential expression
between aberration groups
•FDR
Bioinf (2006)
Methods & software: Sjoerd Vosse (VUmc), Wessel van Wieringen (VU), Mark van de Wiel (VU/VUmc) et al.
Biological feedback: Bauke Ylstra (VUmc) et al.; Database: Floris Sicking (LIACS) et al.
March 2007
Contact: [email protected]