I hope one R genius can help me crack my code problem.
I am performing GSEA form a DeSeq2 analysed object, the past code has worked before with the given dataset, but somehow the KEGG analysis is currently not working for me (Error pasted below). Alongside I am also running GO and Reactome using:
gseGO() and gsePathway ()
Both are working
I work from a server if this is important
library(clusterProfiler)
> library(org.Hs.eg.db)
>
> res_id <- res_id[!duplicated(res_id[c("entrezgene_id")]),]
> res_gsea<- as.vector(res_id$log2FoldChange)
> names(res_gsea)<-res_id$entrezgene_id
>
>
> KEGGgsea <- gseKEGG(geneList = res_gsea,
+ organism = 'hsa',
+ minGSSize = 10,
+ maxGSSize = 1000,
+ pvalueCutoff = 0.05, pAdjustMethod = "BH",
+ verbose = FALSE)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
simpleWarning in file(con, "r"): cannot open URL 'https://rest.kegg.jp/link/hsa/pathway': HTTP status was '403 Forbidden'
Error in file(con, "r") :
cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway'
I hope one R genius can help me crack my code problem.
I am performing GSEA form a DeSeq2 analysed object, the past code has worked before with the given dataset, but somehow the KEGG analysis is currently not working for me (Error pasted below). Alongside I am also running GO and Reactome using:
gseGO() and gsePathway ()
Both are working
I work from a server if this is important