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

sam method in VolcanoPlot checking Log2(x) with incorrect condition #273

Open
steph-robinson opened this issue Mar 22, 2024 · 0 comments
Open

Comments

@steph-robinson
Copy link

if self.dataset.preprocessing_info["Normalization"] is None:

Hi, I noticed this line in the sam method of VolcanoPlot.py checks normalization status of the processing info instead of the Log2 status:

Here's what I suggest it to be instead:
if self.dataset.preprocessing_info['Log2-transformed'] is False:

Additionally, this method doesn't allow s0 to be defined by user, and instead defines constants within itself. Could this be added for users trying to call a moderated t-test and SAM FDR method?

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

No branches or pull requests

1 participant