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

DESeq2 #105

Open
BlueK77 opened this issue Oct 6, 2023 · 1 comment
Open

DESeq2 #105

BlueK77 opened this issue Oct 6, 2023 · 1 comment

Comments

@BlueK77
Copy link

BlueK77 commented Oct 6, 2023

Hi, I've tried to run "run_deseq2" from microbiomeMarker package and "DESeq" form DESeq2 package with the same data set and with defaults parameters with both packages. I expected to have the same results or at least very similar instead they are completely different. I am working with microbiome data (with many zeros) and now I am wondering which of the two package I should believe. Are the default settings of "run_deseq2" optimized for microbiome data? If so, which are those settings?
Kind regards

@Wellington9023
Copy link

First, filtering taxa whose abundance is zero in your OTU table, and then run Deseq() with sfType = "poscounts" , you can get the same result with run_deseq2().

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

2 participants