Ophir et al. BMC Genomics 2010, 11:269 http://www.biomedcentral.com/1471-2164/11/269 Page 8 of 10 Figure 6 Conserved sets of SFPs. An example of five genes with SFPs (green dots) that are conserved between the two mapping populations. Each square is a graph of the log signal ratio between two populations relative to the position of the probe from the 5' end of the UniGene. The five upper squares illustrate the genetic difference between 'Dulce' and PI414723 (PI) and the five lower squares illustrate the genetic difference between PI161375 (PIS) and 'Piel de Sapo' (PS). (D2 - D1)-(P1 - D1)-(P2 - D1) = P − D 2 the intra-PI variation (P1 - D1)-(P2 - D1) = P1 − P2 the intra-'Dulce' variation D2 − D1 2) The ordinary t-statistic of each comparison (con- trast) for each SFP probe was moderated by shrinking its standard error towards a common value borrowed from the gene ensemble by Bayesian as described in Smyth 2004 [28]. Therefore, from equations (2), (3), and (4) we used the moderated-t statistics for the statistical signifi- (2) (3) (4) cance test. The p-value was corrected using Benjamini and Hochberg's method [43] to get an adjusted p-value (or q-value). The B statistic is a Bayesian view of the p-value giving the log odds that an SFP is true (probe signal ratio is sig- nificant). The exact formula of B is described in [44]. SFP validation SFPs were selected randomly for validation from the list of putative SFPs. Based on sequence information from the melon database, primers were designed from 50-100 bp of the SFP using Primer3 software [45]. PCRs were performed from DNA pools of PI414723 and 'Dulce' (PCR conditions: 30 cycles of 30 s at 94°C, 30 s at 58°C, 1 min at 72°C). Sequencing was executed by Macrogen Inc., Korea. Sequence analysis was performed using Vector NTI software (Invitrogen). Only samples that showed good-quality sequences from the two parents were ana-