Question: gseaplot() function of clusterProfiler went wrong
0
gravatar for giuseppe0525
19 months ago by
giuseppe05250 wrote:

Hello, everyone!

1.

I got the error 'Error in if absmax.ES) > absmin.ES)) { :  

missing value where TRUE/FALSE needed' 

when running gseaplot() to visualize the GSEA result.

 

2.

I run the code 'gseaplot(gsea, geneSetID = "mmu03013")'  where gsea is a gseaResult object. The class of gsea is shown as followed:

> class(gsea)
[1] "gseaResult"
attr(,"package")
[1] "DOSE"

The object gsea is created with the GSEA() function, in which geneList(t_isc24) is derived from MArrayLM object using limma package, and TERM2GENE(pathway) is created based on EnrichmentBrowser package. The related codes are shown below:

 

## create pathway

library(EnrichmentBrowser)

gs <- get.kegg.genesets("mmu")

 

$`mmu00020_Citrate_cycle_(TCA_cycle)`
 [1] "104112" "11428"  "11429"  "12974"  "13382"  "14194"  "15926"  "15929"  "170718" "17448"  "17449"  "18293"  "18534"  "18563"  "18597" 
[16] "18598"  "20916"  "20917"  "235339" "239017" "243996" "269951" "56451"  "66052"  "66925"  "66945"  "67680"  "67834"  "68263"  "71832" 
[31] "74551"  "78920

...

> class(gs)
[1] "list"

...

> class(pathway)
[1] "matrix"
  

 

## create t_isc24

library(limma)

probeID <- rownames(ischemic_ebFit$t)
head(probeID)

gene_id_t <- getEG(probeID, "mouse430a2")


colnames(ischemic_ebFit$contrasts)
head(ischemic_ebFit$t)

> head(ischemic_ebFit$t)
              Contrasts
               sham24h_ischemia24h
  1415670_at             -2.400054
  1415671_at             -1.196139
  1415672_at              3.523950
  1415673_at              2.581356
  1415674_a_at           -1.942669
  1415675_at             -3.272687


t_isc24 <- ischemic_ebFit$t[,"sham24h_ischemia24h"]
names(t_isc24) <- gene_id_t
t_isc24 <- sort(t_isc24, decreasing = TRUE)

> class(t_isc24)
[1] "numeric

> head(t_isc24)
   16878    20310    67951    14579    17392     <NA> 
44.58554 28.30740 27.52500 27.31784 26.72206 26.26859 

## GSEA

gsea <- GSEA(geneList = t_isc24, 
     exponent = 1, 
     nPerm = 1000, 
     minGSSize = 10,
     maxGSSize = 1000, 
     pvalueCutoff = 0.05, 
     pAdjustMethod = "BH", 
     TERM2GENE = pathway,
     TERM2NAME = NA, 
     verbose = TRUE, 
     seed = FALSE, 
     by = "fgsea")

 

3.

However, I run the gseaplot() function with another gsearesults object derived from gsekegg() function and it actually worked.

gsekegg <- gseKEGG(t_isc24, organism = "mmu", 
                   keyType = "ncbi-geneid", 
                   exponent = 1,
        nPerm = 1000, 
        minGSSize = 10, 
        maxGSSize = 1000, 
        pvalueCutoff = 0.05,
        pAdjustMethod = "BH", 
        verbose = TRUE, 
        use_internal_data = FALSE,
        seed = FALSE, 
        by = "fgsea")

> class(gsekegg)
[1] "gseaResult"
attr(,"package")
[1] "DOSE"

 

A plot was returned when running gseaplot(gsekegg, geneSetID = "mmu03013").

 

I really appreciate your kindness if you can offer some suggestion on this problem.

 

 

clusterprofiler gsea • 555 views
ADD COMMENTlink written 19 months ago by giuseppe05250

As 'Language "ca" is not one of the supported languages ['en']!' , I cannot list some objects mentioned above.

ADD REPLYlink written 19 months ago by giuseppe05250
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