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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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DESeq2 input for Transcription factor activity inference in bulk RNA-seq #104

Closed t1nnenissen closed 8 months ago

t1nnenissen commented 10 months ago

Hi there,

Thanks for making this amazing toll available!

I have been trying to do a TF activity analysis of my bulk RNA-seq data following this guide: https://saezlab.github.io/decoupleR/articles/tf_bk.html

I have a few questions regarding the output from the DESeq2 analysis.

1. For generating the heatmap - is it appropriate to use the output from the vsd function on the dds data?

2. As input data for generating a plot as seen below (from the tutorial), is it appropriate to the use the 'stat' data generated from the Deseq2 analysis (see below)?

Screenshot 2023-11-28 at 11 38 50 Screenshot 2023-11-28 at 11 41 09

Best, Tinne

PauBadiaM commented 10 months ago

Hi @t1nnenissen,

1) Indeed you can use the vst-transformed counts for the heatmap 2) Yes, to run enrichment analysis from DESeq2 results we recommend to use their stat value since it informs both the direction of change (+ or -) and the significance of the change (the absolute magnitude of the value).

Hope this is helpful!