clusterProfiler (KEGG Enrichment Analysis) error

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7.7 years ago

ta_awwad ▴ 350

Hello everybody, I am currently running RNA_seq pipeline and it was absolutely fine until I reached the KEGG step. first, I have 400 DE genes . I created matrix of ENTREZID and log2foldchange. here is the head of my matrix:

> head(cp_matrix)
     35526      41092      39976      40831      36778      33636 
-0.4144379 -0.6321093 -0.3219794 -2.0373447  2.3645869  0.6998755

then I have run:

kegg_enrich <- enrichKEGG(gene = names(cp_matrix),
                          organism = "fly",
                          pvalueCutoff = 0.05, 
                          qvalueCutoff = 0.10)

and I have the same error message:

No gene can be mapped....
--> return NULL...

any idea how to solve this??

thanks much

RNA-Seq ChIP-Seq KEGG pathway • 4.3k views

ADD COMMENT • link 7.7 years ago by ta_awwad ▴ 350

1

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Maybe it is this issue?

ADD REPLY • link 7.7 years ago by h.mon 35k

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My IDs are already character

class (names(cp_matrix))
[1] "character"
names(cp_matrix)
  [1] "36544"    "39244"    "36420"    "31904"    "34189"    "44149"    "35526"    "41092"   
  [9] "31130"    "32471"    "37815"    "43183"    "45398"    "40850"    "53425"    "40831"