New methods to analyse microarray data that partially lack a reference signal

BMC Genomics

Table 1 Sensitivity, specificity, PPV and NPV of the newly developed analysis methods based on calculated cut-offs per spot.

Analysis method	Test characteristics	MRSA252^a	All spots^b
1 Cut-off based on two times the background	Sensitivity^c	96.90%	86.40%
	Specificity	15.21%	76.68%
	PPV	89.43%	73.64%
	NPV	39.91%	82.34%
2 Cut-off based on reference signal intensities	Sensitivity	50.31%	90.06%
	Specificity	100%	19.79%
	PPV	100%	51.96%
	NPV	21.38%	71.69%
3 Cut-off based on the minimal ratio positivity	Sensitivity	99.98%	98.24%
	Specificity	98.81%	7.85%
	PPV	99.84%	50.86%
	NPV	99.89%	80.90%
4 Cut-off based on two times the background and reference signal intensities	Sensitivity	50.31%	79.15%
	Specificity	100%	81.61%
	PPV	100%	76.13%
	NPV	21.38%	76.41%
5 Cut-off based on two times the background and the minimal ratio of positivity	Sensitivity	96.90%	86.24%
	Specificity	99.24%	77.88%
	PPV	99.89%	74.09%
	NPV	81.24%	82.34%

^a Spots based on MRSA252 ORFs (75% of all spots on the array). Flagged spots of the MRSA252 data set were filtered from the calculations.
To validate the results of the different new analysis methods the MRSA252 spots were also analysed with the new methods and compared with the results obtained with the GACK method and sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the new methods were calculated.
^b All spots representing genes present in MRSA252, N315, MW2, Mu50, NCTC8325, COL and MSSA476.
^c To calculate sensitivity, specificity, PPV and NPV of the new methods, the hybridisation results of six sequenced strains used in the array design were included with the exception of the results of MSSA476. The calculated sensitivity of an analysis method was only based on the specific spots for each strain that were added to the array. So only the MRSA252 spots were taken into account for the sensitivity for the MRSA252 strain. Specificity for a strain could only be calculated based on the strains that were added on the array after the specific strain. These genes have to be divergent, since they were not present in the specific strain. This means that for strain NCTC8325 all 170 genes spotted extra for strains MW2 and MSSA476 should be divergent in the NCTC8325 hybridisations, since MW2 and MSSA476 were added after NCTC8325.

ISSN: 1471-2164