Can subtle changes in gene expression be consistently detected with different microarray platforms?

BMC Genomics

Table 1 Description of the platforms under study.

Platform	Name	#Probes	#Unique UniGene IDs	#Ensembl transcripts *	one/two color	# DEGs (10% FDR)	# DEGs UniGene dataset (N = 10,876)	# DEGs Ensembl dataset (N = 12,744)
ABI	Applied Biosystem- AB1700	35,948	19,013	25,858	one	4	4	5
AFF	Affymetrix – Mouse Genome 430 v2.0 Array	45,101	20,320	23,553	one	130	72	112
AGL	Agilent- WMG G4122A	41,232	20,612	25,845	two	3,051	1,594	2,003
ILL	Illumina- Sentrix Mouse- 6 Expression BeadChip	46,133	19,292	25,629	one	54	19	24
LGTC	Home-spotted 65-mer oligonucleotide arrays (Sigma- Compugen collection)	21,997	15,261	18,104	two	13	22	35
All Platforms			10,876	12,744		-	285**	693**

* More probes could correspond to the Ensembl transcript.
** The number of differential genes obtained comes from the integrated analysis of data from all platforms within one statistical model which takes the platform into account (cf. Discussion section)

ISSN: 1471-2164