Table 1

Example identifier coverages and overlaps between selected chip platforms
Platform Chip Species Identifier Original feat. num. Collapsed feat. num. Merged feat. num. Overlap
Agilent G4112F H. sapiens gene symbols 41078 18575 17981 96.8%
Affymetrix U133Plus2 H. sapiens gene symbols 54675 19798 90.8%
Agilent G4112F H. sapiens gene symbols 41078 18575 16976 91.4%
Affymetrix U133Plus2 H. sapiens gene symbols 54675 19798 85.7%
Illumina HumanRef8v3 H. sapiens gene symbols 24526 21090 80.5%
Agilent G4112F H. sapiens ENTREZ ID 41078 18575 17981 96.8%
Affymetrix U133Plus2 H. sapiens ENTREZ ID 54675 20723 86.8%
Agilent G4112F H. sapiens ENTREZ ID 41078 18575 16976 91.4%
Affymetrix U133Plus2 H. sapiens ENTREZ ID 54675 20723 81.9%
Illumina HumanRef8v3 H. sapiens ENTREZ ID 24526 21090 80.5%
Agilent G4112F H. sapiens Unigene 41078 19712 19163 97.2%
Affymetrix U133Plus2 H. sapiens Unigene 54675 21505 89.1%
Agilent G4112F H. sapiens Unigene 41078 19712 18189 92.3%
Affymetrix U133Plus2 H. sapiens Unigene 54675 21505 84.6%
Illumina HumanRef8v3 H. sapiens Unigene 24526 21153 86.0%
Agilent G4112F H. sapiens ENSEMBL 41078 17899 17574 98.2%
Affymetrix U133Plus2 H. sapiens ENSEMBL 54675 18618 94.4%
Agilent G4112F H. sapiens ENSEMBL 41078 17899 17281 96.5%
Affymetrix U133Plus2 H. sapiens ENSEMBL 54675 18618 92.8%
Illumina HumanRef8v3 H. sapiens ENSEMBL 24526 19291 89.6%
Illumina MouseRef8v2 M. musculus gene symbols 25697 22221 18037 81.2%
Affymetrix M430.2 M. musculus gene symbols 45101 22114 81.6%
Illumina MouseRef8v2 M. musculus ENTREZ ID 25697 22221 18037 81.2%
Affymetrix M430.2 M. musculus ENTREZ ID 45101 22114 81.6%
Illumina MouseRef8v2 M. musculus Unigene 25697 22663 19510 86.1%
Affymetrix M430.2 M. musculus Unigene 45101 22261 87.6%
Illumina MouseRef8v2 M. musculus ENSEMBL 25697 20126 17384 86.4%
Affymetrix M430.2 M. musculus ENSEMBL 45101 17780 97.8%

Several major microarray chip platforms have been tested with virtualArray. The collapsing of probes/probesets was based on gene symbols, ENTREZ ID, Unigene ID or ENSEMBL ID, resulting in different reduced feature numbers (collapsed feature number). When two or three platforms are merged, the feature number is further reduced. However, the fraction of overlap in respect to the single chips was always above 80%.

Heider and Alt

Heider and Alt BMC Bioinformatics 2013 14:75   doi:10.1186/1471-2105-14-75

Open Data