BMC Genomics 2008, 9:230 http://www.biomedcentral.com/1471-2164/9/230 control strains (TRG spots). The latter class, constituted by TRG spots, is of no interest for this evaluation because in all the performed hybridizations these spots will have a present call, preventing the setting of a threshold that optimally discriminates between absent and present calls. For this reason, when the spots are analyzed in separate classes, the TRG spots were not considered, both for hybridizations with the T control or with the mix control. For comparison purposes, discarding TRG spots is not anticipated to bias the results since both control types are expected to behave similarly in relation to this class of spots, producing signals of equivalent intensity, eventu- ally with smaller variance for the mix control due to the pooling effect. To explore differences in AUC, Acc, Sn and Sp values between hybridizations with the T control or the Mix as control, eliminating the effect of different test samples (R or G), we applied the nonparametric Friedman's test [30] and corrected for multiple testing by controlling the False Discovery Rate under or equal to 0.05 through the linear procedure of Benjamini and Hochberg [31]. Abbreviations LR – Log Ratio, R – R6, T – TIGR4, G – G54, TR – genes or spots present in TIGR4 and R6, TG – genes or spots present in TIGR4 and G54, RG – genes or spots present in R6 and G54, TRG – genes or spots present in all reference strains, ROC – receiver operating characteristic, AUC – area under the curve, TP – true positive, FP – false positive, TN – true negative, FN – false negative, Sn – sensitivity, Sp – specificity, Acc – accuracy, aCGH – array based compar- ative genomic hybridization. Authors' contributions FRP, SIA, JM–C and MR conceived the study. SIA per- formed the experiments and FRP analyzed the datasets generated. All authors wrote, revised and approved the final manuscript. Additional material Additional file 1 LR thresholds. Supplementary Table with LR thresholds producing maxi- mum Acc for the 16 array hybridizations. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-9-230-S1.pdf] Acknowledgements FRP and SIA were supported by grants SFRH/BPD/21746/2005 and SFRH/ BD/27518/2006, respectively, from Fundação para a Ciência e Tecnologia, Portugal. FRP is a research member of the Lisbon Epidemiology Consor- tium (CEL) funded by Fundação para a Ciência e Tecnologia, Portugal. Par- tial support for this work was provided by Fundação Calouste Gulbenkian, Fundação para a Ciência e Tecnologia (POCTI/ESP/47914) and by unre- stricted research grants from Pfizer Portugal and Glaxo Smith Kline Portu- gal. 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