Tag: dba.plotProfile

atac seq – Help with error DiffBind

Would you please suggest what wrong in this case? I pretty much run the same code as I used for another data set and didn’t have this error. Thank you so much! result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.count(result) result <- dba.normalize(result) result <-…

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Help with DiffBind Generating report-based DBA object… Error: No valid contrasts/methods specified.

Help with DiffBind Generating report-based DBA object… Error: No valid contrasts/methods specified. 0 Hi all, Would you please suggest what wrong in this case? I pretty much run the same code as before. Thank you so much. result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.count(result)…

Continue Reading Help with DiffBind Generating report-based DBA object… Error: No valid contrasts/methods specified.

Missing samples when using function plotProfile() from DiffBind for ATAC-seq

I have 4 samples which are 4 conditions but when I made this plot, I got only 2 conditions. Here is the code I used: samples <- read.csv(“path/to/sample_sheet_DiffBind.csv”) result <- dba(sampleSheet=samples) result <- dba.blacklist(result) result <- dba.count(result, bParallel=FALSE) result <- dba.normalize(result) result <- dba.contrast(result, minMembers=2) result <- dba.analyze(result) dba.plotProfile(profiles) I…

Continue Reading Missing samples when using function plotProfile() from DiffBind for ATAC-seq

DiffBind: dba.plotProfile() Change sample order

DiffBind: dba.plotProfile() Change sample order 0 Hi, Is it possible to change the order of samples when using dba.plotProfile()? I’ve tried defining them with the samples= parameter, but I haven’t been successful. I’ve made lovely plots (this is a great tool!), but instead of the default order (ex A, B,…

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