Question: padj in DEseq2
0
gravatar for mxlsherry1992
11 months ago by
mxlsherry199230 wrote:

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 • 1.0k views
ADD COMMENTlink modified 11 months ago by Brice Sarver3.5k • written 11 months ago by mxlsherry199230
3
gravatar for ATpoint
11 months ago by
ATpoint38k
Germany
ATpoint38k wrote:

adjusted pvalue means corrected for multiple testing.

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint38k

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

ADD REPLYlink written 11 months ago by mxlsherry199230
1

He just told you, adjusted p-value.

ADD REPLYlink written 11 months ago by Joe17k

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

ADD REPLYlink written 10 weeks ago by MaxF70
1
gravatar for Brice Sarver
11 months ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

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...

ADD COMMENTlink modified 11 months ago • written 11 months ago by Brice Sarver3.5k
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