fixed the bug in scdrs/util.py #76
Merged
Conversation
This file contains 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
When mcp included NaN, significance was not displayed. This is because multipletest()[1] is filled with NaN when p values included NaN, while multipletest()[0] is normal. By modifying to use multipletest()[0], the problem is solved.
|
@martinjzhang I've noticed an issue when using multiple scdrs_groups with scdrs.util.plot_group_stats. Specifically, when some of the group stats contain NaN values, none of the significance values are displayed. While this is a rare case, it can occur, for example, when stratifying group_stats by condition. The cause of this bug seems to be that when p values contains NaN, multipletests()[1] returns NaN while multipletests()[0] returns valid results. Therefore, I've changed to use multipletests()[0] for displaying significance instead. Please review this modification when you have a chance. |
KangchengHou
requested changes
Nov 29, 2023
KangchengHou
approved these changes
Nov 29, 2023
|
looks great and thank you! |
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Outdated suggestions cannot be applied.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.
When mcp included NaN, significance was not displayed.
This is because multipletest()[1] is filled with NaN when p values included NaN, while multipletest()[0] is normal.
By modifying to use multipletest()[0], the problem is solved.
Related to #75