Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

BMC Bioinformatics

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.

ISSN: 1471-2105