Question: clusterProfiler : How works the q-value filtering ? What is a good cutoff ? Is this like an FDR ?
gravatar for ZheFrench
20 months ago by
ZheFrench10 wrote:

Im  using clusterProfile clusterProfiler_3.0.5 on R  3.3.1  as follows :

kegg <- enrichKEGG(entrez_id, organism="hsa", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.2,use_internal_data=FALSE)


I have two questions:

I don't understand how works the pvalue and qvalue. pvalueCutof is just use for filtering on pAdjusted value or raw p-value ?

In my output, I have  lines with a qvalue upper to 0.2 whereas my qvalueCutoff is set to 0.2. Is this a bug or qvalueCutoff is used for another thing than simply filtering here.

What is q-value ? I set to 0.2 (taken from an example) But is it a kind of FDR...?  Kind of relative to that conceptual question about FDR, FDR adjusted p-value and q-value




ADD COMMENTlink modified 20 months ago by Guangchuang Yu990 • written 20 months ago by ZheFrench10
gravatar for Guangchuang Yu
20 months ago by
Hong Kong
Guangchuang Yu990 wrote:

If you set qvalueCutoff = 0.2, it will filter out those larger than 0.2.


pvalueCutoff will restrict p.adjust.



ADD COMMENTlink written 20 months ago by Guangchuang Yu990

Yeah thanks, I made a mistake, end of the day :/

ADD REPLYlink written 20 months ago by ZheFrench10
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