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Question: Clarifications on p-values in enrichResult objects
1
gravatar for enricoferrero
14 months ago by
enricoferrero550
United Kingdom
enricoferrero550 wrote:

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!

ADD COMMENTlink modified 14 months ago by Guangchuang Yu800 • written 14 months ago by enricoferrero550
2
gravatar for Guangchuang Yu
14 months ago by
Hong Kong
Guangchuang Yu800 wrote:

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.

 

ADD COMMENTlink written 14 months ago by Guangchuang Yu800

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

ADD REPLYlink written 14 months ago by enricoferrero550
1

AND, both should be satisfied.

ADD REPLYlink written 14 months ago by Guangchuang Yu800
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