Question: DESeq2: why the independent filtering threshold would come back as NULL please?
0
gravatar for Aurelie MLB
2.2 years ago by
Aurelie MLB290
United Kingdom
Aurelie MLB290 wrote:

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

 

 

rna-seq • 926 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Aurelie MLB290
1
gravatar for Aurelie MLB
2.2 years ago by
Aurelie MLB290
United Kingdom
Aurelie MLB290 wrote:

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 So I guess my code was out of date.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

ADD COMMENTlink written 2.2 years ago by Aurelie MLB290
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