Question

question about the refined outputs from GOfuncR package

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capricygcapricyg ▴ 10

@capricygcapricyg-17892

Last seen 2.4 years ago

United States

Hi Bioconductor Support,

I tried to run the "refine" function from the GOfuncR package and noticed that different GO catetories used different p-value threshold for significance (as shown in the screenshot). My question is: how this threshold was selected? Can I have my own threshold?

Thanks

C. enter image description here


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

GOfuncR • 1.1k views

ADD COMMENT • link 3.0 years ago • updated 2.4 years ago capricygcapricyg ▴ 10

score 0 · Answer 1 · 2021-11-07

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Steffi Grote ▴ 10

@f67b142b

Last seen 9 months ago

Germany, Göttingen

Hi,

the threshold for the significance is based on the FWER, which you can modify using the fwer parameter of the refine function. The p-value that is printed to the console corresponds to this FWER. Since the three GO-domains are analyzed seperately, the same FWER likely corresponds to different p-values for each domain.

The refinement is based to on the p-value and not the FWER, because GO-terms are re-tested for significance after removing genes from significant child-terms (see the elim algorithm as described in Alexa, A. et al. (2006).), and this does not involve a re-calculation of the FWER.

Best, Steffi

ADD COMMENT • link 3.0 years ago Steffi Grote ▴ 10

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Hi Steffi,

My outputs showed that some of the GO terms had quite different p-values after refinement. May I say those GO terms have many genes removed as child-terms? Is there a way to find what genes were removed actually during the refinement?

Thanks a lot.

C.

ADD REPLY • link 2.4 years ago capricygcapricyg ▴ 10