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xzhoulab / iDEA

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
GNU General Public License v3.0
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Output explanations #24

Closed JRWallace closed 2 years ago

JRWallace commented 2 years ago

Hello! Thank you for this package. I am wondering if you have any details or information about how to interpret the outputs from iDEA@gsea. More specifically, what are the annot_coef, annot_var, annot_var_louis, and sigma2_b? This information is probably in the manuscript but I think it would be helpful to have it in the documentation for the package.

annot_id annot_coef annot_var annot_var_louis sigma2_b pvalue_louis pvalue
1 REACTOME_FATTY_ACID_METABOLISM -1.750754 0.09029776 0.1001064 238.8785 3.140330e-08 5.669802e-09
2 REACTOME_GLYCOLYSIS -1.135788 0.13735320 0.1483048 239.1861 3.184886e-03 2.179394e-03
3 REACTOME_INTERFERON_SIGNALING 1.775729 0.07376514 0.0796045 239.3457 3.099353e-10 6.230865e-11

Thanks, Joselynn

YingMa0107 commented 2 years ago

Hi @JRWallace,

Thank you very much for your great suggestions. I have added some interpretations in the tutorial page.

Specifically, the "annot_id" represents the gene set name, "annot_coef" is the estimated gene set enrichment parameter that determines the odds ratio of DE for genes inside the gene set versus genes outside the gene set. "annot_var" is the estimated variance of the annot_coef, "annot_var_louis" is the adjuested variance of the annot_coef by the Louis Method, "sigma2_b" is the scaling parameter. "pvalue_louis" is the pvalue calculated when applying Louis method to calibrate the pvalues while "pvalue" is the common pvalue without Louis Method correction.

Thank you again!

Best, Ying