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3.4 years ago

Hi all, if you know the full name of padj in DESeq2? I know if it corrected p-value, but It should be the abbreviation, so if you know the full name for that?

RNA-Seq • 7.7k views
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3.4 years ago
ATpoint 70k

adjusted pvalue means corrected for multiple testing.

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Hi, yes, but if know what is the full name for padj...just like false discovery rate for FDR.

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He just told you, adjusted p-value.

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Note that the results function automatically performs independent filtering based on the mean of normalized counts for each gene, optimizing the number of genes which will have an adjusted p value below a given FDR cutoff, alpha. Independent filtering is further discussed below. By default the argument alpha is set to 0.1. If the adjusted p value cutoff will be a value other than 0.1, alpha should be set to that value

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3.4 years ago
Brice Sarver ★ 3.7k

A quick Google search finds this post, which outlines it pretty clearly.

Specifically, it looks like the function is calling p.adjust() with method = "BH".