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saezlab / decoupler-py

Python package to perform enrichment analysis from omics data.
https://decoupler-py.readthedocs.io/
GNU General Public License v3.0
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dc.run_mlm only returning data for 1 source #115

Closed aalockhart1 closed 6 months ago

aalockhart1 commented 6 months ago

Hi, When I run the following code: 

dc.run_mlm(
    mat=adata,
    net=progeny,
    source='source',
    target='target',
    weight='weight',
    verbose=True
)

I get the following 2506 features of mat are empty, they will be removed. Running mlm on mat with 308 samples and 11943 targets for 1 sources.

The only source I get data for is JAK-STAT. Any ideas? Thanks in advance

PauBadiaM commented 6 months ago

Hi @aalockhart1,

It looks like you have few overlap hits between the resource progeny and non-zero genes in your mat (decoupler filters out sources with less than 5 target genes in your mat). How many top genes are you using when running dc.get_progeny? I would recommend to increase the number and see if you get better overlap but unfortunately it just seems like your data consists mostly of zeros. Hope this is helpful!

aalockhart1 commented 6 months ago

That worked, thank you!