Question

error running enricher from clusterprofiler

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Yael • 0

@ccb6ce01

Last seen 7 months ago

Israel

Hi, im trying to run enricher() from clusterprofiler and in getting an error "--> No gene can be mapped.... --> Expected input gene ID: GO:0002831,GO:0045184,GO:1901698,GO:0007017,GO:0017076,GO:0033365 --> return NULL..."

this is the code im using and my data.tables:


enrichment_results <- enricher(
  gene = gene_list_inv,
  TERM2GENE = genes2go,
  TERM2NAME = NULL,
  universe = NULL,  # Optionally specify the universe of genes if not using the entire genome
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH")

sessionInfo( )

> enrichment_results <- enricher(
+   gene = gene_list_inv,
+   TERM2GENE = genes2go_2,
+   TERM2NAME = NULL,
+   universe = NULL,  # Optionally specify the universe of genes if not using the entire genome
+   pvalueCutoff = 0.05,
+   pAdjustMethod = "BH"
+ )
--> No gene can be mapped....
--> Expected input gene ID: GO:0002831,GO:0045184,GO:1901698,GO:0007017,GO:0017076,GO:0033365
--> return NULL...

these are the input data.tables:

> print(gene_list_inv)
             GID
          <char>
 1: LOC119360363
 2: LOC119360381
 3: LOC119361995
 4: LOC119361997
 5: LOC119362003
 6: LOC119362007
 7: LOC119362023
 8: LOC119367010
 9: LOC119367016
10: LOC119367018
11: LOC119367024
12: LOC119367043
13: LOC119367043
> print(genes2go_2)
                  GID         GO
               <char>     <char>
      1: LOC119357312 GO:0043229
      2: LOC119357312 GO:0005198
      3: LOC119357312 GO:0044434
      4: LOC119357312 GO:0043226
      5: LOC119357312 GO:0044238
     ---                        
2003725: LOC119348655 GO:0072593
2003726: LOC119348655 GO:0097159
2003727: LOC119348655 GO:0048037
2003728: LOC119348655 GO:0055114
2003729: LOC119348655 GO:0016684

the genes in gene_list_inv do appear in the genes2go_2, there are no space characters either...

can anyone assist?

Thanks

clusterProfiler cluster • 655 views

ADD COMMENT • link 7 months ago Yael • 0

score 0 · Answer 1 · 2024-05-15

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

Last seen 2 days ago

Wageningen University, Wageningen, the …

You should swap the column order in your genes2go_2 data frame; first column should be the GOID (your column GO), the second should be the gene id (your column GID).

Thus: TERM2GENE = genes2go_2[ ,c(2,1) ]

ADD COMMENT • link 7 months ago Guido Hooiveld ★ 4.1k

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Thanks Guido, I tried that too, unfortunately it still isn't working

ADD REPLY • link 7 months ago Yael • 0

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It does for me! Please check that the inputs are in the proper format!

Note that when creating the gene2go input I incorrectly assigned the first 2 genes in your input list gene_list_inv to the genes2go data frame (so that some input genes have a GO annotation). Still an error is reported, but that has to do with the very limited sized input I used (and not with the input not being recognized).

> library(clusterProfiler)
> 
> gene_list_inv <- c("LOC119360363","LOC119360381","LOC119361995","LOC119361997","LOC119362003","LOC119362007","LOC119362023",
+                     "LOC119367010","LOC119367016","LOC119367018","LOC119367024","LOC119367043","LOC119367043")
> 
> ## make FAKE gene-to=GO mapping; use 1st two input LOCs
> genes2go <- data.frame("GID" = c("LOC119360363","LOC119360363","LOC119360363","LOC119360363","LOC119360363",
+                                  "LOC119360381","LOC119360381","LOC119360381","LOC119360381","LOC119360381"),
+                        "GO" = c("GO:0043229","GO:0005198","GO:0044434","GO:0043226","GO:0044238",
+                                 "GO:0072593","GO:0097159","GO:0048037","GO:0055114","GO:0016684") )
> 
>                                 
> enrichment_results <- enricher(
+   gene = gene_list_inv,
+   TERM2GENE = genes2go[ ,c(2,1)],
+   TERM2NAME = NULL,
+   universe = NULL, 
+   pvalueCutoff = 0.05,
+   pAdjustMethod = "BH")
No gene sets have size between 10 and 500 ...
--> return NULL...
>

ADD REPLY • link 7 months ago Guido Hooiveld ★ 4.1k

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It worked!!! Thanks alot, i think something in the gene_list wasnt right...

Thanks agian

ADD REPLY • link 7 months ago Yael • 0