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Hey yall, I'd appreciate any insight on this topic or any resources I can use for further reading
I ran FindMarkers with test.use = "DESeq2" on my pseudobulked data and the results were unexpected. For one cell type, there are 263 genes with a p_val of <0.05, but there are only three genes with p_val_adj of <0.05.
FindMarkers will apply bonferroni correction to calculate the p_val_adj regardless of the test used (right?). But, standalone DESeq will calculate its own p_val_adj with BH. So my question is: Is the p_val reported when using DESeq in FindMarkers report DESeq's pvalue or padj?
I am unsure how to consider the results of my pseudobulk test. In the vignette it looks like non-adjusted p values were compared to the single cell wilcox DE results.
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Hey yall, I'd appreciate any insight on this topic or any resources I can use for further reading
I ran FindMarkers with test.use = "DESeq2" on my pseudobulked data and the results were unexpected. For one cell type, there are 263 genes with a p_val of <0.05, but there are only three genes with p_val_adj of <0.05.
FindMarkers will apply bonferroni correction to calculate the p_val_adj regardless of the test used (right?). But, standalone DESeq will calculate its own p_val_adj with BH. So my question is: Is the p_val reported when using DESeq in FindMarkers report DESeq's pvalue or padj?
I am unsure how to consider the results of my pseudobulk test. In the vignette it looks like non-adjusted p values were compared to the single cell wilcox DE results.
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