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Published 20 hours ago • verified publisher icon nf-core

treatment vs control

Open elffairy90 opened this issue 3 years ago • 1 comments

Hi , after analysis, the comparison is control vs treatment, how I do make it treatment vs control if I need to run the pipeline again. Thank you!

Best regards, Jenny

elffairy90 avatar Dec 14 '20 03:12 elffairy90

Hi @elffairy90 ! Did you manage to figure this out? Thanks!

drpatelh avatar Jan 25 '21 19:01 drpatelh

Hi @elffairy90 ! Thanks for reporting and apologies for the delay in responding! We have decided to strip out the differential analysis that has been in this pipeline until v1.2.2. This was for a number of reasons but primarily because it isn't possible to properly encode all of the experimental labels with a single column like group. The more formal statistical analysis should be performed downstream and we have another nf-core workflow in development at the moment that we can add this functionality to instead: https://github.com/nf-core/differentialabundance

drpatelh avatar Nov 18 '22 12:11 drpatelh