User: tlaguna

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tlaguna10
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New User
Location:
IMB Mainz
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2 years, 3 months ago
Joined:
2 years, 4 months ago
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Posts by tlaguna

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Comment: C: Why do I get different GO term sizes using the same gene universe for 2 analyses
... Thank you for the good explanation James! Before it was not clear to me how the 'conditional' test works, now it is crystal clear. ...
written 2.3 years ago by tlaguna10
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Why do I get different GO term sizes using the same gene universe for 2 analyses with GOstats?
... Checking different results of hypergeometric tests using GOstats, I found that, surprisingly, using the same gene universe for 2 different gene enriched sets, there are different number of GO term sizes for the same GO term:   An example Gene set enr: 1480 GOBPID Pvalue OddsRatio ...
gostats hypergeometric test written 2.3 years ago by tlaguna10 • updated 2.3 years ago by James W. MacDonald50k
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Comment: C: about columm "size" in out of hyperGtest ( Gostat package)
... I think the goal in every forum is to not have duplicated threads, that's why I reopen a threat of 7 years ago. Indeed, the question was not answered.  But ok, will do. ...
written 2.3 years ago by tlaguna10
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Answer: A: about columm "size" in out of hyperGtest ( Gostat package)
... I think what Greg was trying to say is that if you do 2 analysis using the same gene universe, it is not clear why he obtains different universe counts for the same GO term. I did not realize that happens until a collaborator pointed it out. I am also confused about this difference. Marc, can you ex ...
written 2.3 years ago by tlaguna10
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Answer: A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
... I have to say that I had the same problem using the release version of GOstats in Bioconductor. I realized that AnotationDBI, GO.db, and other packages to which GOstats depend on, were not updated, and after updating them the problem was solved. Just in case someone has the same issue... ...
written 2.3 years ago by tlaguna10

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