Both GSEA method currently filter out terms with missing values in p-value column.
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res <- res[!is.na(res$pvalue),] |
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res <- res[!is.na(res$pvalue),] |
This might not be ideal since cases with unbalanced gene-level statistic values, pval, padj, NES, log2err are set to NA, which further prevent users that would like to view the complete results without any cutoffs by setting pValueCutoff=1. Could we have a separate argument like reportNA to ensure advanced users could access the results?
5: In fgseaMultilevel(pathways = pathways, stats = stats, ... :
There were 2 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 10000)
Both GSEA method currently filter out terms with missing values in p-value column.
DOSE/R/gsea.R
Line 88 in 1ce3c6f
DOSE/R/gsea.R
Line 324 in 1ce3c6f
This might not be ideal since cases with unbalanced gene-level statistic values, pval, padj, NES, log2err are set to NA, which further prevent users that would like to view the complete results without any cutoffs by setting
pValueCutoff=1. Could we have a separate argument likereportNAto ensure advanced users could access the results?