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

 write.csv(summary(kegg),file=paste0(c(getwd(),dir_pathway,"DESEQ_KEGG_ENRICHMENT.csv"),collapse="/"))

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 13 months ago by Guangchuang Yu800 • written 13 months ago by ZheFrench10
1
gravatar for Guangchuang Yu
13 months ago by
Hong Kong
Guangchuang Yu800 wrote:

If you set qvalueCutoff = 0.2, it will filter out those larger than 0.2. https://github.com/GuangchuangYu/DOSE/blob/master/R/enricher_internal.R#L147

 

pvalueCutoff will restrict p.adjust.

 

 

ADD COMMENTlink written 13 months ago by Guangchuang Yu800

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

ADD REPLYlink written 13 months ago by ZheFrench10
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