1. Peak list *.cod Column 1: peak rank Col2: chromosome Col3: peak start Col4: peak end Col5: peak strand (currently all + for ChIP-chip) Col6: peak length Col7: maxM/P = maximal TileMap-MA statistic or maximal HMM posterior probability of all the probes within the peak Col8: probe (genomic coordinate) where the maxM/P is obtained Col9: FDR = false discovery rate based on MaxM/P Col10: local_FDR = local false discovery rate based on MaxM/P Col11: maxFC(log2) = maximal log2(IP/Control) fold change with the peak. Col12: probe (genomic coordinate) where the maxFC is obtained. Col13: sumM/P = integration of MA statistics or HMM probabilities, obtained by adding the statistics of all good probes in the peaks together. If no outlier filtering was applied in the tilemapv2_importaffy step, good probes = all probes. If outlier filtering was applied, good probes = non-outlier probes and probes for which MA or HMM statistics could be computed. Col14: number of good probes used in computing sumM/P Col15: sumM/P_FDR = false discovery rate based on sumM/P Col16: sumM/P_local_FDR = local false discovery rate based on sumM/P Col17: library_id = array id. For example, if you use mouse genome tiling 7 array set, 1=chip A, 2=chip B, ..., 7 = array F. Col18: group_name = genome assembly in the data bar file. 2. *.fc.bar: log2(IP/Control) fold change for each probe. 3. *.ma.bar or *.hmm.bar: TileMap MA statistic or HMM posterior probability for being a binding event for each probe.