The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

BMC Bioinformatics

Table 2 Correlation between expression levels measured by RT-PCR and Affymetrix GeneChip on the AML dataset, after use of different pre-processing methods.

Gene symbol	Probe set ID	MAS	dChip	RMA	GCRMA
*EVI1*	215851_at	0.34	0.52	0.63	0.29
	221884_at	0.64	0.87	0.88	0.45
P8	209230_s_at	0.09	0.15	0.16	0.00
*PRDM1*	217192_s_at	0.53	0.57	0.55	0.53
*TRKA*	208605_s_at	0.66	0.77	0.75	0.63
*PRDM2*	205277_at	0.21	0.25	0.28	0.25
	203057_s_at	0.56	0.56	0.59	0.58
	203056_s_at	0.57	0.59	0.59	0.55
	216433_s_at	0.33	0.42	0.45	0.12
*MEIS1*	204069_at	0.88	0.90	0.90	0.86
*HOXA9*	214651_s_at	0.90	0.90	0.91	0.89
	209905_at	0.91	0.91	0.90	0.90
*HOXA7*	206847_s_at	0.80	0.77	0.80	0.89
	206848_at	0.01	0.02	0.02	0.04
*CEBPA*	204039_at	0.61	0.61	0.63	0.58
*GMCSF*	210229_s_at	0.20	0.32	0.10	0.15

ISSN: 1471-2105