Question: ReactomePA - Pathway analysis for DE porcine genes
0
gravatar for thomasjenner333
18 months ago by
thomasjenner3330 wrote:

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. 

clusterprofiler reactomepa • 533 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by thomasjenner3330
Answer: ReactomePA - Pathway analysis for DE porcine genes
1
gravatar for Guangchuang Yu
18 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

how about:

rpa <- enrichPathway(gene=geneSS, pvalueCutoff=1, qvalueCutoff=1, readable=T, organism="pig")
ADD COMMENTlink written 18 months ago by Guangchuang Yu1.1k

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.

ADD REPLYlink written 18 months ago by thomasjenner3330
1

maybe you would find the blog post useful.

ADD REPLYlink written 18 months ago by Guangchuang Yu1.1k

Thanks you.

ADD REPLYlink written 18 months ago by thomasjenner3330
1

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).

ADD REPLYlink written 18 months ago by Guido Hooiveld2.5k
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