Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add additional donor normalization options #45

Closed
rmarkello opened this issue Jun 19, 2019 · 0 comments · Fixed by #90
Closed

Add additional donor normalization options #45

rmarkello opened this issue Jun 19, 2019 · 0 comments · Fixed by #90
Labels
enhancement New feature or request

Comments

@rmarkello
Copy link
Owner

The issue

The current method for normalizing between-donor microarray expression differences prior to collapsing across donors is to use a scaled robust sigmoid correction procedure. This is cool and good and I think the right move, but is perhaps a bit non-standard so providing alternative options would be nice.

Proposed solution

Adding a parameter to abagen.get_expression_data() like donor_norm and adding the ability to z-score the data would be cool. That way someone could run either:

abagen.get_expression_data(atlas, donor_norm='srs')

or

abagen.get_expression_data(atlas, donor_norm='zscore')

and get back interpretable results.

My only concern with this solution is that the number of optional parameters for abagen.get_expression_data() is getting a bit overwhelming! It might be worthwhile making this function a "workflow" (with a CLI, too?) and refactoring some of the other functions to be more modular / tool-oriented so that a user could construct an alternative workflow if they wanted.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant