**10**wrote:

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**?

**2.2k**• written 9 months ago by tjiagoM •

**10**

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

0

tjiagoM • **10** wrote:

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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modified 9 months ago
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Guido Hooiveld • **2.2k**
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9 months ago by
tjiagoM • **10**

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Guido Hooiveld • **2.2k** wrote:

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.

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?

1

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).

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