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guokai8 / scGSVA

scGSVA: Perform GSVA for single cell RNA seq
GNU General Public License v3.0
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Input issue #11

Open enBiter opened 1 year ago

enBiter commented 1 year ago

Hi, I have an issue with trying to load the SingleCellExperiment objects. Please check the report that uses 5k PBMC dataset from 10X:

scGSVA input issue.pdf (skip to page 22 for stuff that did not work for me)

I've tried both loading the SCE from HDF5 and from filtered_feature_bc_matrix and both resulted in errors. I've also tried to convert the counts and logcounts matrices to dgCmatrix and it did not help. Conversion to Seurat also did not work.

apal6 commented 1 year ago

Hi,

Were you able to fix this issue? I am facing the same problem

guokai8 commented 1 year ago

Hi @enBiter , I am sorry for the late reply. If you want to use the "SingleCellExperiment" object, you should have the counts data in the obj, so please check the "counts(obj)" command to see if it works. Best, K