Helena L. Crowell

First round of comments below! Note that many are suggestions and not strictly required (e.g., "consider..."). Please comment back here with what has/not been addressed how/why not, or any comments...

Thanks for the speedy action. I can see changes have been made in the package's GH repo, however, in order for these to go through to Bioc, you need to...

Again, I can see this on your GH. However, if a build has been triggered, you'd see a message here from the bioc-issue-bot, which is not the case. You also...

Yes, that all looks correct. Now, when you want to make changes, you should push to both the origin and upstream remote. I.e., commit -m “…” — push origin —...

Did you try doing this? The package being built [here](http://bioconductor.org/spb_reports/rifiComparative_buildreport_20220722142514.html) is still v0.99.0 whereas your Github repo [DESCRIPTION](https://github.com/CyanolabFreiburg/rifiComparative/blob/main/DESCRIPTION) has v0.99.2.

Hm. I can only see a single build report from 21 days ago [here](https://github.com/Bioconductor/Contributions/issues/2718#issuecomment-1192832084). Did you push upstream as explained [here](https://contributions.bioconductor.org/git-version-control.html#new-package-workflow)? I.e., something like ``` git add ... git commit...

First round of comments below! Note that many are suggestions and not strictly required (e.g., "consider..."). Please comment back here with what has/not been addressed how/why not, or any comments...

**Major comment** I understand you rewrote some code for `IFAA()` and `MZILN()` to accept a `SummarizedExperiment` as input as opposed to two separate tables. However, there's little sense in doing...

Hm. Why not return a long-form table instead? This would be more standard and much easier to view/filter as opposed to 5 separate matrices. E.g., something like: ``` DataFrame with...

Thank you for trying to address this. ...I think there has been a misunderstanding or perhaps my comments above where contradictory/confusing; apologies for that. Similar to other statistical methods/tests, in...