search

perslab / CELLEX

CELLEX (CELL-type EXpression-specificity)
GNU General Public License v3.0
37 stars 9 forks source link

[BUG]: eso.compute error. #37

Closed myylee closed 6 months ago

myylee commented 6 months ago

Hi there,

Thanks for the great package.

While running the eso.compute(), I encountered an error like this.

Screen Shot 2024-04-26 at 11 20 12 AM

I did install all the requirements as in the requirement.txt file, which was also suggested in previous issues.

I was able to run CELLEX with the mousebrain_vascular_cells example, just not my dataset.

I'd greatly appreciate any thought on what is causing the error and how might one solve it.

Thanks!

Best regards, Michelle

myylee commented 6 months ago

I think part of the reason is that after eso = cellex.ESObject(data=data_fil, annotation=md_format_fil, verbose=True), my eso.summary_data.variance has a shape of (0,8). But I don't know why the variance matrix was not calculated on my dataset.

myylee commented 6 months ago

Nvm, I solved it. It was because my panda dataframe is a sparse instead of dense.

tstannius commented 6 months ago

Hi myylee

Glad to hear that you solved the issue 😄

Yes, most modern sc datasets use sparse data now, which CELLEX was not written to work with.

Best, Tobi