Hi all. I'm about to submit a paper and I have used the functions available
in the "GOstats" package to do most of the work for me. I have a question
about multiple testing and the output of significant GO-terms that you get
using the GOHyperG function. I quote R. Gentleman as he states it in the
helpfile.

 

"First and most importantly it is not clear how to do any form of p-value

 correction in this case. The tests are not independent and the

 underlying structure of the GO graph present certain problems that

 still need to be addressed."

 

I have also red the very informative previous discussion on bioC list from
2004 http://files.protsuggest.org/biocond/html/3732.html

 

If I want to motivate that I do not correct for multiple testing in my paper
and mention that I am aware of that and that I see the results only as a
guide to common "themes" in my data, does anyone have any suggestion of any
references dealing with this issue that I can use? 

 

Best regards

 

Johan L

 

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Johan Lindberg

Royal Institute of Technology

AlbaNova University Center

Stockholm Center for Physics, Astronomy and Biotechnology

Department of Molecular Biotechnology

Visiting address:

Roslagstullsbacken 21, Floor 3

106 91 Stockholm, Sweden

Delivering address:

Roslagstullsbacken 30B

104 06 Stockholm, Sweden

Phone (office) +46 8 553 783 44

Fax + 46 8 553 784 81

http://www.ktharray.se/

http://www.arrayadvice.se/

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