I some how, figure out the manual to reproduce the same plots for my data.
I'm working with non-model organism it doesn't have a annotation information or package for GO/KEGG analysis.
I had ~4 experimental setup, after edgeR analysis based on the padjustvalue lessthan 0.05 I chosen significantly expressed differential genes include both Up/Down regulated genes.
I chosen, zebrafish annotation for my data, performed Gene Set enrichment analysis works very well. While KEGG enrichment step I'm getting "no term enriched under specific pvalueCutoff..." any sugesstions ? In this case, how do I get KEGG annotation?
> library(org.Dr.eg.db) > kegg_organism = "dre" > kk2 <- gseKEGG(geneList = KGgenelist, organism = "dre", nPerm = 10000, minGSSize = 3,maxGSSize = 800,pAdjustMethod = "none",keyType = > "ncbi-geneid") > preparing geneSet collections... > GSEA analysis... > no term enriched under specific pvalueCutoff... > Warning messages: > 1: In .GSEA(geneList = geneList, exponent = exponent, minGSSize = minGSSize, : > We do not recommend using nPerm parameter incurrent and future releases > 2: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize, : > You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm > argument in the fgsea function call.