Benchmarking different DESeq2 design models
1
0
Entering edit mode
11 months ago
jdhindsa1999 ▴ 20

Hello,

I have RNA time-course data and am looking to benchmark two different DESeq2 models I want to use. One design models time as a categorical variable, while the other design models time as a continuous variable. I am wondering if anyone knows of any R packages or methods to compute values such as AUROC to compare these two models performance in detecting DEGs.

Thank you

RNA-sequencing differential-gene-expression DESeq2 R • 418 views
ADD COMMENT
0
Entering edit mode

Do you have a set of validated DEGs (from another source of data) that can serve as the ground truth for your DESeq2 models? Is this in-silico RNA-seq data or real experimental data?

ADD REPLY
0
Entering edit mode
11 months ago
jv ▴ 470

To generate AUROC statistics requires both a set of defined true positives and true negatives to serve as the "ground truth" to compare model performance against. This is typically achieved via cross validations when developing models.

For an example from a related post see https://www.biostars.org/p/271616/#271616

ADD COMMENT

Login before adding your answer.

Traffic: 706 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6