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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:
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.
The text was updated successfully, but these errors were encountered:
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()
likedonor_norm
and adding the ability to z-score the data would be cool. That way someone could run either:or
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.The text was updated successfully, but these errors were encountered: