DiffBind error with DBA_DESEQ_GLM and warning with DBA_EDGE_GLM
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@elisabetta-manduchi-575
Last seen 7.1 years ago
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
a4 DiffBind a4 DiffBind • 670 views
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