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

BMC Bioinformatics

Table 1 Detection concordance between AB microarrays and TaqMan^® assays in UHR and Brain.

UHR, site 1	TP	TN	FP	FN	Sensitivity	Specificity
TaqMan	789	59	0	0	100	100
AB microarrays	605	48	11	184	76.68%	81.36%
Brain, site 1	TP	TN	FP	FN	Sensitivity	Specificity
TaqMan	744	104	0	0	100	100
AB Microarrays	581	79	25	163	78.09%	75.96%

For each platform, sample and site, a gene is declared detected (present) if it is detected according to the platform specifications, in more than half of the replicates. Concordance between detection calls are presented in these tables for UHR and Brain samples in site 1 (Sensitivity = true positive rate, Specificity = 1-false positive rate).

ISSN: 1471-2105