Hello, I'm using DiffBind version 1.2.0 with R 2.15.0 on linux. I've created a dba object data.deseq and run: > data.deseq = dba.count(data.deseq,score=DBA_SCORE_TMM_READS_EFFECTIVE,bRemoveDuplic ates=T,bCorPlot=F) > data.deseq = dba.contrast(data.deseq,categories=DBA_TISSUE,block=DBA_FACTOR) So data.deseq looks like this: 24 Samples, 212418 sites in matrix: ID Tissue Factor Condition Replicate Intervals 1 A2 Arch 2 M 1 212418 2 A3 Arch 3 F 2 212418 3 A4 Arch 4 M 3 212418 4 A5 Arch 5 F 4 212418 5 A7 Arch 7 F 5 212418 6 D2 Descending 2 M 1 212418 7 D3 Descending 3 F 2 212418 8 D4 Descending 4 M 3 212418 9 D5 Descending 5 F 4 212418 10 D7 Descending 7 F 5 212418 11 A10 Arch 10 F 6 212418 12 A11 Arch 11 M 7 212418 13 A12 Arch 12 M 8 212418 14 A13 Arch 13 M 9 212418 15 A14 Arch 14 M 10 212418 16 A15 Arch 15 F 11 212418 17 A17 Arch 17 F 12 212418 18 D10 Descending 10 F 6 212418 19 D11 Descending 11 M 7 212418 20 D12 Descending 12 M 8 212418 21 D13 Descending 13 M 9 212418 22 D14 Descending 14 M 10 212418 23 D15 Descending 15 F 11 212418 24 D17 Descending 17 F 12 212418 1 Contrast: Group1 Members1 Group2 Members2 Block1Val InBlock1 Block2Val InBlock2 1 Arch 12 Descending 12 10 2 11 2 Block3Val InBlock3 Block4Val InBlock4 Block5Val InBlock5 Block6Val InBlock6 1 12 2 13 2 14 2 15 2 Block7Val InBlock7 Block8Val InBlock8 Block9Val InBlock9 Block10Val InBlock10 1 17 2 2 2 3 2 4 2 Block11Val InBlock11 Block12Val InBlock12 1 5 2 7 2 1. When I then try to run: data.deseq = dba.analyze(data.deseq,method=DBA_DESEQ_GLM,bSubControl=F,bCorPlot=F) I get the following error: Error in .local(object, ...) : None of your conditions is replicated. Use method='blind' to estimate across conditions, or 'pooled-CR', if you have crossed factors. In addition: Warning message: Unable to use tagwise dispersion estimates with GLM I'm not clear why it's not seeing the replicates, since I have 12 for each of Arch and Descending. Am I setting things up incorrectly? 2. Note that I've also analyzed the same dba with method DBA_EDGER_GLM. This ran, but gave me the following warning on which I'm unclear Warning message: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence and it only found 154 significant intervals out of the over 212000 input sites, which seems too low. Anybody can advice on the above? Thanks, Elisabetta