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.

Sign up for GitHub

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

Jump to bottom

empirical p-values for glmnet multivariate results #17

Open
9 of 10 tasks
mschubert opened this issue Aug 2, 2015 · 1 comment
Open
9 of 10 tasks

empirical p-values for glmnet multivariate results #17

mschubert opened this issue Aug 2, 2015 · 1 comment
Labels
in progress todo

Comments

@mschubert
Copy link
Collaborator

prerequesites

  • map all scores to specific set of pathways
  • use same pathway set input for glmnet

kinds of models

  • pathways
  • mutations and pathways as one input (to compare mut to pathways)
  • mutations + pathways (as in, formula syntax - to compare which pathways add most on top)

generation of null models

  • null models: 100 repetitions, shuffled labels
  • null models: 1000 repetitions, shuffled labels
  • real model: one repetition

calc

  • empirical p-values for models
  • bar plots for best models (as defined with p-val)
@mschubert mschubert added the todo label Aug 2, 2015
@mschubert
Copy link
Collaborator Author

shuffling labels does not introduce enough variability - if e.g. 1 cell line out of 15 is sensitive, will fit in 1/15th of models

will not be a part of the paper, maybe look at this separately

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
in progress todo
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@mschubert