Question

What's the difference between p.adjust and qvalue?

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tjiagoM ▴ 10

@tjiagom-13123

Last seen 6.9 years ago

In the result of an enrichGO() we have two columns, p.adjust and qvalue. I guess p.adjust is the pvalue modified after considering FDR, but then what actually is the qvalue?

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ADD COMMENT • link updated 6.9 years ago by Guido Hooiveld ★ 3.9k • written 6.9 years ago by tjiagoM ▴ 10

score 1 · Answer 1 · 2017-05-26

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Guido Hooiveld ★ 3.9k

@guido-hooiveld-2020

Last seen 19 hours ago

Wageningen University, Wageningen, the …

From the help page (?enrichGO):

pAdjustMethod: one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

Note: default = "BH".

qvalue: alternative approach/algorithm to calculate FDR/control for multiple testing. For more details see the package qvalue here.

Note: default value is 0.2.

ADD COMMENT • link 6.9 years ago Guido Hooiveld ★ 3.9k

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Exactly, I saw that, but isn't that the same meaning as of an adjusted p-value? Because calculations of FDR are meant to change the pvalue, right?

ADD REPLY • link 6.9 years ago tjiagoM ▴ 10

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Yep, the aim of all 'FDR algorithms' is the same, but how they exactly work differ between the algorithms. See e.g. this thread + links conceptual question about FDR, FDR adjusted p-value and q-value for an easy accessible overview, and confusion regarding nomenclature. The thread @ Biostars here also discusses this question (and links to the same BioC thread).

ADD REPLY • link 6.9 years ago Guido Hooiveld ★ 3.9k

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Ok, the package mentions that they are not creating adjusted pvalues. I will look with more attention, thanks.

ADD REPLY • link 6.9 years ago tjiagoM ▴ 10