Skip to content

Commit

Permalink
Updated DE figure
Browse files Browse the repository at this point in the history
  • Loading branch information
Gammerdinger authored Apr 29, 2024
1 parent c335bf9 commit df5e642
Showing 1 changed file with 2 additions and 3 deletions.
5 changes: 2 additions & 3 deletions lessons/04a_design_formulas.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,10 +17,9 @@ Approximate time: 30 minutes
The final step in the differential expression analysis workflow is **fitting the raw counts to the NB model and performing the statistical test** for differentially expressed genes. In this step we essentially want to determine whether the mean expression levels of different sample groups are significantly different.

<p align="center">
<img src="../img/de_theory.png" width="600">
<img src="../img/Differential_expression.png" width="900">
</p>

*Image credit: Paul Pavlidis, UBC*



The [DESeq2 paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8) was published in 2014, but the package is continually updated and available for use in R through Bioconductor. It builds on good ideas for dispersion estimation and use of Generalized Linear Models from the [DSS](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005660/) and [edgeR](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/) methods.
Expand Down

0 comments on commit df5e642

Please sign in to comment.