Error in GSEA function of clusterProfiler on R
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18 months ago

Hello everyone I just met some problem with GSEA when I run the clusterProfiler. Can anyone help me how to fix the problem, although the data still could be processed (I'm not so sure the data could be used under those error message.

Follow my code

geneList_organism = "mmu"                                                                                                                                            
           kk2 <- gseKEGG(organism     = geneList_organism,
           geneList     = geneList,
           nPerm        = 10000,
           minGSSize    = 3,
           maxGSSize    = 800,
           pvalueCutoff = 0.05,
           pAdjustMethod = "none")******

Output error message:

> preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Warning messages:

 1.  In .GSEA(geneList = geneList, exponent = exponent, minGSSize = minGSSize,  :
  We do not recommend using nPerm parameter incurrent and future releases
 2.  In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize,  :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.
 3. In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (16.25% of the list).
 4. In serialize(data, node$con) :  'package:stats' may not be available when loading
 5. In serialize(data, node$con) :  'package:stats' may not be available when loading
RNA-Seq R GSEA clusterProfiler • 2.2k views
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Check this post

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I already try that method than before. But it’s just show the other error message said It’s not suitable for hsa GSEA( but it’s really so wired that I do not type any associating with human species). So I wonder to know have any method to fix that.

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kk2 <- gseKEGG(geneList=geneList, 
             keyType = "ENTREZID", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = org.Mm.eg.db, 
             pAdjustMethod = "none")

It will process the following error message.

Reading KEGG annotation online:

Reading KEGG annotation online:

Reading KEGG annotation online:

fail to download KEGG data... Error in KEGG_convert("kegg", keyType, species) : ENTREZID is not supported for has ...

Then I try to exchange the code of following

gsepathway <- gseKEGG(geneList=geneList, 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = org.Mm.eg.db, 
             pAdjustMethod = "none")

It will process this error message

Error in .GSEA(geneList = geneList, exponent = exponent, minGSSize = minGSSize, : unused argument (OrgDb = new("OrgDb", .xData = <environment>))

How should I adjust my code?

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Hi Jimmy, first of all you are not getting an error - this is a warning message. Error would be a break in the code. Here the code performs but tells you that something is fishy. Here is what I can say to your warnings:

Warning 1 - 2: I am still trying for myself how to change the fgseaSimple to fgseaMultilevel within clusterProfiler's gseKEGG function. However unfortunately with little success so far ... i think the problem is that fgsea was further developed recently and the fgseaMultilevel was implemented and is now considered to perform better than fgseaSimple while clusterProfiler did not integrate this novel development. Again, idk if that is true or not but I think it would explain the warning comming from the fgsea function. Maybe someone else in this community can help out here.

Warning 3: Exactly what the warning message says. Check here for more info.

Warning 4-5: As you nPerm is relatively large this could be the problem. Try some smaller nPerm like 1000 or 2000 and see if the warning still appears.

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17 months ago

Thanks, Hannes

Warning 1/2 I think warning one and two seems like a long term problem with those involved in this field. Exactly I'm not so sure that I could put this figure on my review. In fact, I also ran out the same data to GSEA tools, but the data looks so different in both. I'm so worried about that.

Warning 3 Thanks for your hint. I think that won't be my problem again.

Warning 4/5 I also checked some user code and found that seems not so necessary to type this parameter. But I will take your advance to adjust THX.

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