Question: ReactomePA / Reactome: GSEA error message
gravatar for martin.busch
12 months ago by
martin.busch0 wrote:

Hi everyone,

I am sorry to ask another question, however, there is an error message that keeps me puzzled. When passing over a list of human entrez IDs to reactomePA for GSEA using

result <- gsePathway(anaData, nPerm=10000, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE)

Rstudio becomes busy and cannot finish computation. When I manually stop it I get the error message:

Warning message:
In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize,  :
  There are duplicate gene names, fgsea may produce unexpected results

How can I pass over parameters like maxSize=500 and which parameter can I use to avoid duplicate gene names, although the entrez IDs are unique? Seems like the mapping yields duplicate gene names?!

Thank you so much in advance for your help,



P.S: Input look like this

> head(anaData,10)
    1301     3371     4069    57537    11081     5764   114899     2331     1303     7060 
6.198340 4.505550 3.962765 3.753962 3.461323 3.148910 3.075820 3.034261 3.010098 2.880258 
> length(anaData)
[1] 11317
reactome gsea reactomepa fgsea • 377 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by martin.busch0

Could you also paste the resul of any(duplicated(names(anaData)))? This is what is checked at fgsea.

ADD REPLYlink written 12 months ago by assaron150

Thank you so much for your comment - in fact I was pretty suprised to see that the result was true - something that should not have happened. There was some mapping involved and it seems that multiple ensembl IDs can be mapped to one entrez ID. I thought that I had this sorted out. Anyways, not it works pretty fine! Thanks a lot!

ADD REPLYlink written 12 months ago by martin.busch0
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