Independent Filter returns null value with attr(DESeq2Res, 'filterThreshold')

Question

[Kevin]

I am following along with this tutorial but using different data:

https://www.huber.embl.de/users/klaus/Teaching/DESeq2-Analysis.pdf

I am at the independent filtering part and haven't had any issues in the previous parts. The part of the code that gives me an issue if this:

DESeq2Table<-nbinomWaldTest(DESeq2Table)
DESeq2Res<-results(DESeq2Table,pAdjustMethod="BH")
table(DESeq2Res$padj<0.1)
attr(DESeq2Res,'filterThreshold')

The 'table' line returns results indicating ~5000 DE genes and ~25500 non-DE genes. But, when running the 'attr' line of that chunk it returns a value of 'Null' and I'm not sure why. I'm also a little confused on where 'filterThreshold' comes from in the first place since I don't see anything about it in the attr rdocumentation page.

Edit: viewing the attributes from DESeq2Res I can see this:

$metadata
$metadata$filterThreshold
45.70778% 
0.3646421 

but I don't know why this isn't reported when calling attr(DESeq2Res,'filterThreshold')

Answer 1

[ATpoint]

This tutorial is very old (2014), probably they moved this from an attribute to the current location in the metadata. Not sure whether the results object back in the day was still the same class it is today.

Please read the manual:

http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#independent-filtering-of-results

metadata(res)$filterThreshold is the command.