Hello everyone I just met some problem with GSEA when I run the clusterProfiler. Can anyone help me how to fix the problem, although the data still could be processed (I'm not so sure the data could be used under those error message.
Follow my code
geneList_organism = "mmu" kk2 <- gseKEGG(organism = geneList_organism, geneList = geneList, nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, pAdjustMethod = "none")******
Output error message:
> preparing geneSet collections... GSEA analysis... leading edge analysis... done... 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. 3. In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (16.25% of the list). 4. In serialize(data, node$con) : 'package:stats' may not be available when loading 5. In serialize(data, node$con) : 'package:stats' may not be available when loading