Skip to content

Update analysis example: Switch WGCNA dataset to something that doesn't have technical replicates #373

Description

@cansavvy

Background

#364 (comment)
There's some technical replicates in SRP133573.

Problem

We could deal with replicates by collapsing them, but I think this example is already pretty long and complicated as it is (even though it is an advanced topics example). I think we can switch this out for a dataset that is less complicated and then deal with the collapsing replicates issue separately.

What potential "gotchas" do we know of?

The dataset should be sufficiently large (bigger than 15) but not so large someone couldn't run it locally.
For reference

What are the recommended next steps?

Step 0) After #363 and #364 are merged, this can be addressed. (Easier to take it one step at a time).
Step 1) Find a suitable dataset replacment
Step 2) Try running it in the notebook. If there's not an R^2 above 0.80 than probably no to that dataset.
Step 3) Change module explorations -- see how the plots look.
Step 4) If that dataset otherwise looks good, update all the wording and dataset descriptions.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Fields

    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions