Comments (4)
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Hi Angelus,
It seems you are using the python scripts which are deprecated. Could you try to rerun the analysis using the scDRS CLI and let us know how it goes? https://martinjzhang.github.io/scDRS/reference_cli.html#compute-score
Thank you,
Martin
from scdrs.
from scdrs.
Hi Angelus,
If you are using log normalized data (size factor + log1p), you need to turn off the raw count flag flag_raw_count False
and the filtering flag --flag_filter False
. Maybe the filtering flag is the reason that scDRS removed many genes/cells.
Also, please double-check that the expression matrix doesn't contain negative values.
Best,
Martin
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Related Issues (20)
- Update dependencies of scDRS
- Gene weights or without gene weights HOT 3
- compute-score is not reading .gs file properly HOT 2
- custom gene set ? HOT 2
- The graphs from a single result and multiple results are inconsistent HOT 13
- Subsetting cells for downstream analysis. HOT 1
- TypeError: '<' not supported between instances of 'str' and 'float' HOT 3
- About compute-score
- Is it reasonable to use human' geneset on mouse scRNAseq data? HOT 2
- TypeError: plot_group_stats() got an unexpected keyword argument 'plot_kws' HOT 16
- trait=z_score: skipped due to small size (n_gene=5, sys_time=116.1s) HOT 1
- AssertionError when running quick test after installation HOT 7
- The 'n_fdr_0.2' number of all group is 0 HOT 7
- Interpreting scDRS score when comparing cell-type subclusters HOT 1
- Using geneset from SMR result HOT 1
- ValueError: too many values to unpack (expected 2) HOT 8
- Converting GWAS catalog .tsv file to gene set HOT 3
- Preprocessing: killed running scdrs compute-score HOT 4
- tcell.facs.annot.h5ad without GENE name HOT 2
- use scdrs in a tissue seemlingly unrelated with the disease HOT 4
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