padj in DEseq2

Question

[mxlsherry1992]

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?

Answer 1

[ATpoint]

adjusted pvalue means corrected for multiple testing.

[mxlsherry1992]

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

[Joe]

He just told you, adjusted p-value.

[MaxF]

http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#p-values-and-adjusted-p-values

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

Answer 2

[Brice Sarver]

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".

EDIT: I thought you wanted more info than what ATpoint provided, but I think they've answered your question...