ReactomePA - Pathway analysis for DE porcine genes
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@thomasjenner333-15064
Last seen 3.7 years ago

Hi,

I'm trying to do pathway analysis for DE porcine genes generated using DESeq2. 

(A) I used package "clusterprofiler" to convert gene symbols to enterzids using the following code:

gg = bitr(m1, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Ss.eg.db")

geneSS <- as.vector(gg$ENTREZID)

(B) Then I implemented 'enrichPathway' function to obtain enriched pathways. The following is the code I used, but it failed to generate the enriched pathways. 

rpa <- enrichPathway(gene=geneSS, pvalueCutoff=0.05, readable=T, organism="pig")

head(as.data.frame(rpa))

[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust   

[7] qvalue      Count      

<0 rows> (or 0-length row.names)

I was able to get a list of KEGG pathways using "erichKEGG". But, I couldn't do the same with ReactomePA. Can anyone help solve this? Thanks in advance. 

reactomepa clusterprofiler • 867 views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

how about:

rpa <- enrichPathway(gene=geneSS, pvalueCutoff=1, qvalueCutoff=1, readable=T, organism="pig")
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Hi Yu!

Thank you for responding. I tried what you've suggested, and got a list of pathways. Could you please explain why the previous parameters didn't work? Thanks once again.

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maybe you would find the blog post useful.

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Thanks you.

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Likely because Guangchuang did not specify any significance cutoff (he set the cutoffs for both p-value and q-value to 1, i.e. no significance filtering), and you set the p-value cutoff at 0.05 (which is apparently too strict for your experiment).

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