Effect of various normalization methods on Applied Biosystems expression array system data

BMC Bioinformatics

Table 3 Significantly differentially expressed genes concordance.

	TP	TP rate	TN	FP	FDR	FN
TaqMan	2283	0	261	0	0	0
Quantile	1415	61.98	140	101	7.14	888
Median	1374	60.18	142	99	7.79	929
Scale	1354	59.31	144	97	7.76	949
VSN	1393	61.02	142	99	7.69	910
Loess	1402	61.41	139	102	7.84	901

Genes detected in both samples by TaqMan^® assays (761) are used for this comparison. t-test is used to detect significantly differentially expressed genes, controlling FDR at 5% level. We compare the results from each normalization method, for all sites, with the ones from TaqMan^® assays keeping track of up/down regulation in each platform.

ISSN: 1471-2105