Dear all,
I have been using the gseGO function from clusterProfiler to perform gene set enrichment analysis with a ranked list of genes. However, when I try to reproduce the analysis using compareCluster, passing the same gene list as a single cluster and specifying fun = "gseGO", I obtain similar but not identical results. Some Gene Ontology terms appear in one result but not in the other, and vice versa.
Here is the code I used:
Using gseGO
gse <- gseGO(geneList = gene_list,
ont = "ALL",
keyType = "ENSEMBL",
minGSSize = 3,
maxGSSize = 800,
pvalueCutoff = 0.05,
verbose = TRUE,
OrgDb = "org.Hs.eg.db",
pAdjustMethod = "fdr")
Using compareCluster
compareCluster(geneClusters = list(a1 = gene_list),
pvalueCutoff = 0.05,
ont = "ALL",
keyType = "ENSEMBL",
OrgDb = "org.Hs.eg.db",
fun = "gseGO",
minGSSize = 3,
maxGSSize = 800,
verbose = TRUE,
pAdjustMethod = "fdr")
Has anyone encountered this issue before? What could explain the discrepancies between the two approaches?
Thank you in advance for your insights!
Best regards,
Dear all,
I have been using the gseGO function from clusterProfiler to perform gene set enrichment analysis with a ranked list of genes. However, when I try to reproduce the analysis using compareCluster, passing the same gene list as a single cluster and specifying fun = "gseGO", I obtain similar but not identical results. Some Gene Ontology terms appear in one result but not in the other, and vice versa.
Here is the code I used:
Using gseGO
Using compareCluster
Has anyone encountered this issue before? What could explain the discrepancies between the two approaches?
Thank you in advance for your insights!
Best regards,