https://github.com/microbiome/OMA/issues/824 #794
Conversation
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
Co-authored-by: Muluh <[email protected]>
Co-authored-by: Tuomas Borman <[email protected]>
…is: "Correspondance" → "Correspondence" (#792) Co-authored-by: Tuomas Borman <[email protected]>
Signed-off-by: Daena Rys <[email protected]>
0xMuluh
requested review from
TuomasBorman,
antagomir and
Copilot
and removed request for
Copilot
antagomir
approved these changes
Dec 8, 2025
Comment on lines
+20
to
+21
| #' By default \code{scater::calculateMDS} keeps only the \code{ntop = 500} | ||
| #' most variable features. When rarefaction is enabled (\code{niter > 0}) the |
Member
There was a problem hiding this comment.
does the R code throw a warning of this if it does not use all features? (if data has more than 500)
Contributor
There was a problem hiding this comment.
As we have mia::getMDS and mia::addMDS, we could set the default to no filtering. At least, I have not heard that variance filtering is commonly used in MDS in microbiome context (or then authors of papers have not explicitly stated that)
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Outdated suggestions cannot be applied.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.
No description provided.