BUG fix independent filtering #243
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
BorisMuzellec
force-pushed
the
fix_index_error_in_lowess
branch
from
de9d2cb
to
8fcf5c1
Compare
BorisMuzellec
changed the title
BorisMuzellec
requested review from
maikia,
arthurPignetOwkin and
mandreux-owkin
as code owners
umarteauowkin
approved these changes
Feb 27, 2024
There was a problem hiding this comment.
Thanks a lot @BorisMuzellec for this PR, looks good to me !
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Outdated suggestions cannot be applied.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.
Reference Issue or PRs
Fixes #242
What does your PR implement? Be specific.
This PR fixes a bug in
DeseqStats._independent_filteringcaused by lowess. More precisely:As this bug was not caught by the CI, we add a test case on a synthetic dataset with 50 genes, on which we compare the output of PyDESeq2 with those of the R package DESeq2. In particular, this test case fails without the above fixes.