Repository navigation
harmonizing differential expression output - #273
Merged
Merged
Conversation
… the comparison string and return the dataframe only; adjust tests and notebook calls accordingly
vbrennsteiner
changed the title
vbrennsteiner
added
breaking-change
vbrennsteiner
requested review from
lucas-diedrich and
mschwoer
and removed request for
lucas-diedrich
September 1, 2026 11:41
lucas-diedrich
approved these changes
Sep 1, 2026
lucas-diedrich
left a comment
lucas-diedrich
left a comment
Collaborator
There was a problem hiding this comment.
thanks for standardizing!
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
PR for harmonizing differential expression output
As discussed with @lucas-diedrich, differential expression results should be standardized to allow integrating the new empirical Bayes moderated t-test implementation, as well as standardized downstream visuals that consume differential expression outputs.
Right now, differential expression functions have diverging output formats. This is a bad starting point for implementing new differential expression modules, and a problem for downstream visualizations depending on standardized results.
result_dfcomparison_name,results_dict), where the dict contains "protein" "proteoform" and "peptide" result dataframes.comparison_name,results_df)The goal of this PR is to apply minimal changes to harmonize all three methods to return a single dataframe with standardized columns + method specific columns (like e.g. proteoform values for AlphaQuant)