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Question: Clarifications on p-values in enrichResult objects
1
gravatar for enricoferrero
22 months ago by
enricoferrero570
Switzerland
enricoferrero570 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 22 months ago by Guangchuang Yu1.0k • written 22 months ago by enricoferrero570
2
gravatar for Guangchuang Yu
22 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k 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 22 months ago by Guangchuang Yu1.0k

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 22 months ago by enricoferrero570
1

AND, both should be satisfied.

ADD REPLYlink written 22 months ago by Guangchuang Yu1.0k
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