[DimRed] True features baseline evaluated twice

openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics

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[DimRed] True features baseline evaluated twice #803

Closed lazappi closed 1 year ago

lazappi commented 1 year ago

[x] I have checked that this issue has not already been reported.
[x] I have confirmed this bug exists on the main branch of openproblems.

I think that now that the data loaders return logCPM normalised expression in adata.X the true_features and true_features_logCPM baseline methods for the dimensionality reduction task are now identical and we should only use one of them (or modify true_features to use raw counts?).

scottgigante-immunai commented 1 year ago

You're right -- all of the true_features except the logCPM version can/should be removed -- but I'd like to check that it's performing as expected in the next run before I do so.

scottgigante-immunai commented 1 year ago

Closed in #816