Changes after initial draft

VallejosGroup / BASiCSWorkflow

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Changes after initial draft #19

Closed catavallejos closed 4 years ago

catavallejos commented 4 years ago

Removed refs to simpleSingleCell as there is a redirection notice to OSCA
Further simplified the QC section to avoid duplication with the methods section (e.g. to explain that metrics are used to detect doublets, etc).
Gene-level QC suggests that thresholds require detailed exploration of gene-level metrics. However, we don't have any. Should we change this?

alanocallaghan commented 4 years ago

Yeah point 3 is really jarring now that you mention it. I think the wording can probably be toned down (it sounds extremely intricate currently) and a few figures added to demonstrate the filters chosen and why

catavallejos commented 4 years ago

I agree! I will create an issue to track this.

catavallejos commented 4 years ago

As discussed in https://github.com/catavallejos/BASiCS/issues/175, the use of newBASiCS_Data was removed. I made a first attempt to rewrite the relevant section, but I will probably need to revise the text tomorrow.
I think that running BASiCS_MCMC and running convergence diagnostics in two separate sections (one population; two populations) breaks the flow of the paper. I plan to re-structure the text to run both MCMCs at the same place and do convergence diagnostics together. The analysis can then be separated between the one/two populations cases as it's done now.

catavallejos commented 4 years ago

Of course, feel free to object the second point!

alanocallaghan commented 4 years ago

No I agree, I found it was a bit confusing that things go from QC -> MCMC -> convergence -> analysis -> 2nd dataset -> some filtering -> MCMC -> convergence -> etc

catavallejos commented 4 years ago

Great! I will make the change tomorrow

catavallejos commented 4 years ago

Closing this issue and starting a new one to track changes after the latest draft.