A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

BMC Genomics

Table 3 Comparison of the six algorithms, using the microarray hybridization data from the Sakai sequenced strain. The result of using each algorithm were compared to BLASTN data and are shown below.

	Cut-off	TP	FP	TN	FN	Sensitivity	Specificity	M-Score
	0.50	5285	2	416	41	99.23	99.52	99.25
Naïve	0.33	5297	6	412	29	99.45	98.56	99.39
cut-off	0.25	5302	8	410	24	99.55	98.09	99.44
	0.20	5308	12	406	18	99.66	97.13	99.48
	0.10	5316	64	354	10	99.81	84.69	98.71
GENCOM*		5238	2	416	88	98.34	99.52	98.43
GACK**	EPP = 50	5137	1	417	189	96.45	99.76	96.69
	EPP= 0	5261	1	417	65	98.78	99.76	98.85
Prowollik		5277	1	417	49	99.07	98.76	99.13
MKD***		5297	6	412	29	99.45	98.56	99.39
Mixture	Bimodal	5296	8	413	30	99.44	98.80	99.39
	Trimodal	5244	1	417	82	98.46	99.76	98.55

The number of genes estimated as correctly conserved (True positives, TP), genes identified as conserved but actually are variable (false positives, FP), genes identified as correctly variable (true negatives TN), and genes identified falsely as variable (false negative FN), are given. The sensitivity, specificity, and M-Score are also calculated, where the sensitivity = TP/(TP+FP), specificity = TN/(FP+TN), and M-Score = Sensitivity*prevalence + Specificity*(1-prevalence)
* Institute of Food Research method (GENCOM)
** Genotyping Analysis by Charlie Kim method (GACK)
*** Minimum Kernel Density method (MKD)

ISSN: 1471-2164