Comments (6)
Hi Martin,
Thank you for sending me over the .gs file. I've fixed the issue now, but still don't know what the problem was. I haven't changed anything since last time but it seems to work now. Sorry I can't provide you with analytics and suggest any causes at the moment. I'm getting really interesting results from the down stream analysis though, so thank you very much for developing the program and I hope there's more features to come.
from scdrs.
Thank you @HJ234 and good to hear that you are getting interesting results. We are actively developing the packages. I hope we can release some cool features real soon!
from scdrs.
Hi,
Thank you for reporting this issue. I couldn't identify the cause based on just the .log file. Could you send us a minimal reproducible example (e.g., your zscore file) and also let us know which version of scDRS you are using?
from scdrs.
Hi, thanks for the quick reply. I've sent the zstat file I've been using to "[email protected]" and I'm using scDRS 1.0.2.
from scdrs.
Hi @HJ234
Thank you for sharing the .zscore file. I ran scdrs munge-gs
on your .zscore
file but couldn't reproduce the issue. I sent you the code and the generated .gs
file via email.
This suggests that your zscore file is fine. But I am afraid I still couldn't identify the cause of the issue. Are you using Linux? Could you try to reinstall scDRS using virtualenv
(e.g., https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1588662166 for a tutorial)? If the issue persists, I can push a version of scDRS with more diagnostic information and ask you to run the new version on your data to hopefully identify the issue.
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Hi, Thank you for the great program. I'm trying to run scDRS on one trait, but I seem to get no gene sets after munging with scdrs munge-gs
Call: scdrs munge-gs \ --zscore-file SLE.genes.out.zstat.tsv \ --weight zscore \ --n-min 10 \ --n-max 1000 \ --out-file munge_top1000Z.gs --zscore-file loaded: n_gene=19025, n_trait=1 (sys_time=0.0s) Print info for the first 3 traits and first 10 genes Traits ['SLE'] SAMD11 [1.037] NOC2L [1.1508] KLHL17 [1.5457] PLEKHN1 [2.8403] PERM1 [3.0402] HES4 [2.3732] ISG15 [2.2022] AGRN [2.7473] RNF223 [2.6844] C1orf159 [3.9652] --zscore-file have values above 1 or below 0. Seems fine. Finish munging 1 gene sets (sys_time=0.0s)
The resulting file looks like the following
Would you know what the problem is? Thanks
--zscore-file loaded: n_gene=62787, n_trait=0 (sys_time=0.0s)
Print info for the first 3 traits and first 10 genes
Traits []
PSRC1,-9.289225811 []
AL592148.3,-7.992844093 []
MIA3,-7.120338886 []
TCF21,-6.520148163 []
SLC22A1,-6.220870419 []
NOS3,-6.197266755 []
NBEAL1,-6.112940111 []
ICA1L,6.017449523 []
LIPA,5.811769649 []
AL359922.2,5.799499614 []
Warning: zscore-file values are all between 0 and 1.
Do you know what causes this?
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Related Issues (20)
- Multiple testing correction on downstream analysis HOT 2
- Adjusting for donor effects HOT 1
- GWAS traits and a control traits HOT 12
- tutorial-Quick start ——full_score.gz HOT 1
- Considerations for single cell splicing data HOT 2
- Error when adata.obs_names can be interpreted as integers HOT 2
- "skipped due to small size" error HOT 9
- Please help with scDRS for the plant Arabidopsis thaliana HOT 15
- scdrs compute-score output HOT 4
- Convert Seurat object to h5ad file HOT 10
- Remove NA values in corr anlaysis
- munge-gs input format HOT 2
- Error in scdrs perform-downstream --group-analysis HOT 4
- scRNA data input HOT 6
- perform-downstream outputs zero significant cells HOT 1
- plot_group_stats() got an unexpected keyword argument 'plot_kws' HOT 15
- turning off fdr correction HOT 1
- error metaclass conflict HOT 1
- Issues Plotting UMAP from quick start tutorial HOT 1
- gene weights for the control genes HOT 5
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