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AlexsLemonade / refinebio-examples

Example workflows for refine.bio data
https://www.refine.bio
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Analysis Updates: Restructure validate-differential-expression #112

Open cansavvy opened 4 years ago

cansavvy commented 4 years ago

Right now, validate-differential expression is made up of two notebooks. One that sets up a practice dataset to compare to, and the second that does the actual comparison. We have to think about how to restructure this module and it's set up notebook with the impending restructuring of the refinebio-examples #106

cansavvy commented 4 years ago

At this point, the validate-differential-expression structures is a bit confusing because it involves two notebooks and one of which isn't actually needed from the users point of view:

validate_differential_expression_adv_topics_00_author_de.Rmd - sets up what kind of results a user might want to compare to refinebio data. validate_differential_expression_adv_topics_01.Rmd - Does the actual comparison.

A user who is actually interested in using this notebook, would only need the files from the "author_de" notebook to run the examples but then they would really just replace our author_de files with their own files. So I'm not sure how to make this more clear as well as set up a better file format so perhaps the "author_de" notebook is a bit hidden since its not meant to be an example on it own.

cansavvy commented 4 years ago

I was thinking about this, I think the easiest solution is to turn validate_differential_expression_adv_topics_00_author_de.Rmd into a script that is source() called by validate_differential_expression_adv_topics_01.Rmd. We make it clear to users that this step can be deleted when they are importing their own dataset for comparison.

Related to this, I think the Using this example with your own data section will need to be much more extensive in this situation.