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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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Equivalent variable of t-value from limma in Deseq2 generated DEGs results #70

Closed Diennguyen8290 closed 1 year ago

Diennguyen8290 commented 1 year ago

Hi,

Many thanks for the cool tool.

Please may I ask whether we can use DEGs results from DESeq2 pipeline as the input for Activity inference with Weighted Mean?

[contrast_acts <- run_wmean(mat=deg, net=net, .source='source', .target='target', .mor='weight', times = 100, minsize = 5)]

I was wondering if stat value of Deseq2 generated DEGs results can be used for that purpose.

Thank you.

Kind regards, Dien

PauBadiaM commented 1 year ago

Hi @Diennguyen8290,

Thanks for the kind words! Yes, the stat value of Deseq2 can be used for enrichment

Cheers!

Diennguyen8290 commented 1 year ago

Fab, many thanks @PauBadiaM