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!

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.

Dear teacher Yu: I have a question. As you said, sometimes it may fail to calculate qvalue and then the column will be set to NA without filtering. However, why "enrichGO" sometimes fail to calculate qvalue? what should we do advoid this case happening? And why the column will be set to NA without filtering? If fail to calculate qvalue, why not "enrichGO" results just set to NULL.