Table 7

Matching results for the data sets using various matching procedures
Chin TCGA I TCGA II Taylor I Taylor II
platform details
manufacturer CN UCSF Agilent Agilent Agilent Agilent
probe type CN BAC oligo oligo oligo oligo
manufacturer GE Affymetrix Affymetrix Agilent Agilent Affymetrix
probe type GE oligo oligo oligio oligo oligo
before matching
# samples 89 55 55 49 49
# CN features 2149 234416 234416 223697 223697
# GE features 10757 18528 35582 393 15478
after distance matching
# CN and GE features 10757 18528 35582 393 15478
after distanceAny matching (< 10000 bp)
# CN and GE features 190 18179 34620 389 15254
# CN features per gene (average) 1.04 2.92 2.88 4.36 2.87
after distanceAny matching (< 100000 bp)
# CN and GE features 1921 18480 35424 393 15468
# CN features per gene (average) 1.13 24.33 23.84 27.97 24.47
after overlap matching
# CN and GE features 1734 17426 32135 7 14900
after overlapAny matching (> 0%)
# CN and GE features 1734 17426 32135 7 14900
# CN features per gene (average) 1.13 8.91 8.63 1 9.86
after overlapAny matching (> 0.10%)
# CN and GE features 1585 17424 32123 5 14898
# CN features per gene (average) 1.10 8.91 8.63 1 9.85
after overlapPlus matching
# CN and GE features 1879 18405 35197 349 15381

For the distanceAny and overlapAny the average number of DNA copy number features that contribute to the composition of the final DNA copy number signature is reported. This is one for all other methods.

van Wieringen et al.

van Wieringen et al. BMC Bioinformatics 2012 13:80   doi:10.1186/1471-2105-13-80

Open Data