I want to gseGO() provided by clusterProfiler R package. My gene list is the unregulated markers from a cluster generated by UMAP. The number is log2 fold change.
str(head(cluster7.genes))
Named num [1:6] 2.14 1.81 1.76 1.71 1.67 ...
- attr(*, "names")= chr [1:6] "10082" "9353" "53353" "55553" ...
cluster7.enriched <- gseGO(geneList = cluster7.genes, OrgDb = org.Hs.eg.db, keyType = "ENTREZID", ont = "BP", pvalueCutoff = 1, verbose = FALSE)
Warning messages:
1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
There are duplicate gene names, fgsea may produce unexpected results.
2: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
All values in the stats vector are greater than zero and scoreType is "std", maybe you should switch to scoreType = "pos".
But I don't know why it returns errors even when the pvalueCutoff
is 1. Do I need to change scoreType
to "pos"
to solve this error? If so, how to do it since I can't see any relevant parameters available in gseGO()
for me to change? Thanks.
You are right. I obtained the gene list based on the filter "log2 fold change > 0.25", so my gene list has only positive value. Now that when I remove the filter to obtain the gene list again, as my gene list contains negative value, it works now.
Thanks so much.
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