github上的问题,问了两个问题,这是其中第二个:
Meanwhile, when I fed the ENTREZID to enrichKEGG, it show me two unreasonable results:
kegg_enrich = enrichKEGG( gene = new_ids$ENTREZID, organism = 'hsa', keyType = 'ncbi-geneid', pvalueCutoff = 0.05, #pAdjustMethod = 'BH', #qvalueCutoff = 0.2, use_internal_data = FALSE )
head(kegg_enrich) ID Description GeneRatio BgRatio pvalue p.adjust qvalue hsa04380 hsa04380 Osteoclast differentiation 14/281 128/7299 0.0003817040 0.04767338 0.04508266 hsa04070 hsa04070 Phosphatidylinositol signaling system 12/281 99/7299 0.0003875885 0.04767338 0.04508266
I noted that only 281 genes are remained(there are 700+ genes in my list). In case that there is something wrong wtihin my gene list, I also tried my list with DAVID. It gave me reasonable results. So this is my second question, why enrichKEGG cannot recognize my geneids?