Search
Question: Clarifications on p-values in enrichResult objects
1
gravatar for enricoferrero
2.1 years 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 2.1 years ago by Guangchuang Yu1.0k • written 2.1 years ago by enricoferrero570
2
gravatar for Guangchuang Yu
2.1 years ago by
Guangchuang Yu1.0k
China/Guangzhou/Southern Medical University
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 2.1 years 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 2.1 years ago by enricoferrero570
1

AND, both should be satisfied.

ADD REPLYlink written 2.1 years ago by Guangchuang Yu1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 208 users visited in the last hour