Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ci(dry-run): Set up dry run to use latest version of R and bioc + fix volcano plots #124

Merged
merged 2 commits into from
May 24, 2024

Conversation

tonywu1999
Copy link
Contributor

@tonywu1999 tonywu1999 commented May 17, 2024

Motivation and Context

We're getting dry run issues. I couldn't reproduce the issue locally, so I suspect there's an issue with the environment of R we're running with.

We also ran into an issue during May Institute where volcano plots have an x-axis label of log10 fold change despite using log2 fold change. FC cutoff labels were also based on log 10 instead of log 2.

Changes

  • Fixed code to use the log FC base rather than the log p-value base for volcano plot labels.
  • Update bioc version used in dry run builds. The mapping can be found here

Testing

  • Verified plots look correct locally
  • Build runs correctly

Checklist Before Requesting a Review

  • I have read the MSstats contributing guidelines
  • My changes generate no new warnings
  • Any dependent changes have been merged and published in downstream modules

@tonywu1999 tonywu1999 changed the title ci(dry-run): Set up bioc version to use latest version of R and bioc ci(dry-run): Set up dry run to use latest version of R and bioc + fix volcano plots May 17, 2024
@tonywu1999 tonywu1999 merged commit 9f1caa8 into devel May 24, 2024
1 check passed
@tonywu1999 tonywu1999 deleted the dry-run branch May 24, 2024 17:32
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants