Clarifications on p-values in enrichResult objects
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enricoferrero ▴ 580
@enricoferrero-6037
Last seen 22 hours ago
Switzerland

In clusterProfiler, enrichResult objects have three columns for p-values: pvalue, p.adjust and qvalue.

1. What is the difference between p.adjust and qvalue?

2. On what columns are the pvalueCutoff and qvalueCutoff filters performed?

3. if qvalueCutoff operates on column qvalue, why are rows with a NA q-value not removed?

Thanks!

clusterProfiler reactomepa dose • 994 views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

1. see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html and https://bioconductor.org/packages/release/bioc/html/qvalue.html

2. p.adjust and qvalue

3. Sometimes it may fail to calculate qvalue and then the column will be set to NA without filtering.

 

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Thanks! Are pvalueCutoff and qvalueCutoff combined with an AND or an OR? In other words, do both or either conditions need to be satisfied?

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AND, both should be satisfied.

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