virtualArray: a R/bioconductor package to merge raw data from different microarray platforms

Heider, Andreas; Alt, Rüdiger

doi:10.1186/1471-2105-14-75

BMC Bioinformatics

Table 1 Example identifier coverages and overlaps between selected chip platforms

From: virtualArray: a R/bioconductor package to merge raw data from different microarray 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	17981	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	17981	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	19163	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	17574	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	18037	81.6%
Illumina	MouseRef8v2	M. musculus	ENTREZ ID	25697	22221	18037	81.2%
Affymetrix	M430.2	M. musculus	ENTREZ ID	45101	22114	18037	81.6%
Illumina	MouseRef8v2	M. musculus	Unigene	25697	22663	19510	86.1%
Affymetrix	M430.2	M. musculus	Unigene	45101	22261	19510	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%.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com