Skip to content
GitLab
  • Menu
Projects Groups Snippets
  • /
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in / Register
  • SRP-pipeline SRP-pipeline
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 5
    • Issues 5
    • List
    • Boards
    • Service Desk
    • Milestones
  • Merge requests 2
    • Merge requests 2
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Schedules
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Packages & Registries
    • Packages & Registries
    • Container Registry
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Repository
  • Wiki
    • Wiki
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • bird_pipeline_registry
  • SRP-pipelineSRP-pipeline
  • Merge requests
  • !30

De seq2 formula

  • Review changes

  • Download
  • Email patches
  • Plain diff
Merged Philippe BORDRON requested to merge DESeq2-formula into master Sep 16, 2020
  • Overview 0
  • Commits 3
  • Changes 4

Description

An hidden way that allow to ignore factors or/and plate effect if needed. User must know what he does when using it. This is a proposal, so fell free to comment this PR (ping @eric.charpentier)

How to use it

In order to ignore factor or plate effect, user must add a "normalizationOptions" entry in the comparisons part of the project in the config.json. The entry must describes a list that contains "--ignore-plate-effect" or/and "--ignore-batch-effect".

Example:

{
    ...
    "comparisons": {
        "TestProject": {
            ...
            "normalizationOptions" : ["--ignore-plate-effect"],
            ...
        }
    }
}
Assignee
Assign to
Reviewer
Request review from
Time tracking
Source branch: DESeq2-formula