DESeq2: why the independent filtering threshold would come back as NULL please?

Question

[Aurelie MLB]

Hello,

I am trying to run DeSeq2 on a new dataset.

I have a LOT of differentially expressed genes and when I type attr(RES,"filterThreshold") the result is NULL, which I think means that the independent filtering probably could not take place.

How can this happen please?

Should I be worried? Is it fixable please?

Many thanks

Answer 1

[Aurelie MLB]

Hello,

I have found the answer to my question. In the updated vignette, it is explained that the filtering threshold can be obtained by:

metadata(RES)$filterThreshold.

RES being what is returned by the "results" function. So I guess my code was out of date.

Thanks

[Andrés Ribone]

Watch out the final dot!

Thank you!