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BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
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No significant time-varying pathways in MouseCortex Data #20

Open mjoppich opened 3 years ago

mjoppich commented 3 years ago

Hi,

i have been trying to test Tempora on the MouseCortex.RData object, running the commands listed on the Readme.md page.

However, after running IdentifyVaryingPWs, the function calls returns that there were no significant pathways found. In your paper, however, there are several significant pathways printed.

Now I wonder whether the EM genesets changed this dramatically, or whether I am doing something seriously wrong?

I'd appreciate any suggestions!

Thanks,

Markus

mjoppich commented 3 years ago

I downloaded the publication gmt-file Mouse_GOBP_AllPathways_no_GO_iea_August_01_2019_symbol.gmt .

Still IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05) reports No temporally varying pathways detected. Please try running IdentifyVaryingPWs with a more relaxed p-value cutoff.

The remaining processing steps should be similar to the processing described in the methods of the paper:

cortex_tempora <- CalculatePWProfiles(cortex_tempora, 
                gmt_path = gmt_file,
                method="gsva", min.sz = 10, max.sz = 500, parallel.sz = 1)

cortex_tempora <- BuildTrajectory(cortex_tempora, n_pcs = 6, difference_threshold = 0.01)

Is this desired behaviour?

jordan841220 commented 1 year ago

@mjoppich Same situation here. Have you found any solution?

Thanks.