Table 2.

Description of data sets

	Affymetrix	Agilent	Illumina
Background RNA	HeLa complex cRNA	Human Osteosarcoma (MG-63) purchased from Ambion (Cat. # 7868)	Human Liver purchased from Ambion (Cat. # 7960)
Spike-in production	30 cDNA clones isolated from a lymphoblast cell line, eight artificially engineered, four eukaryotic controls from the polyA spike control kit	In vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A gene	In vitro transcription of cloned bacterial and viral genes
Background correction	RMA	Background subtraction and spatial-detrending	Local background subtraction
Normalization	RMA	Normalized to the 75th percentile on each microarray	Quantile normalization

This table gives a brief comparison of the three data sets used in this analysis.