Question: Does "FRY gene set tests" is possible using a DESEQ2 style analysis ?
0
gravatar for Aurora
21 months ago by
Aurora10
Aurora10 wrote:

Hi !

After a DESEQ2 style analysis I wanted to use the fry function from "roast " (Rotation Gene Set Tests ) in the limma package  to perform a pathway analysis. But I wonder if it is possible or not ?

Have a beautiful day !

Thank you

 

 

deseq2 fry gene tests • 269 views
ADD COMMENTlink modified 21 months ago by Michael Love26k • written 21 months ago by Aurora10
Answer: Does "FRY gene set tests" is possible using a DESEQ2 style analysis ?
2
gravatar for Michael Love
21 months ago by
Michael Love26k
United States
Michael Love26k wrote:

We don't have any gene set testing methods implemented in DESeq2. So if the gene set method uses p-values or LFCs directly, you can use the output of DESeq2. But for roast, you need to use limma.

ADD COMMENTlink written 21 months ago by Michael Love26k

Ty ! Thanks a lot !

ADD REPLYlink written 21 months ago by Aurora10
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