Unable to use compareCluster function with GSEA for three sets of genelists

[aishwarya-gondane]

Hi,

I am using the latest version of ClusterProfiler (4.0.5) and R version is 4.1.1. I am trying to use clusterCompare function on three gene sets. str(InputList) List of 3 $ rankedGeneList1: Named num [1:501] 10.11 9.45 9.45 6.86 6.73 ... ..- attr(, "names")= chr [1:501] "HMGB2" "HMGB2" "HMGB2" "OAZ1" ... $ rankedGeneList2: Named num [1:899] 15.74 9.7 9.12 9.12 6.3 ... ..- attr(, "names")= chr [1:899] "COX6A1" "HMGB2" "HMGB2" "HMGB2" ... $ rankedGeneList3: Named num [1:1451] 16 15.9 11.6 10.6 10.6 ... ..- attr(*, "names")= chr [1:1451] "COX6A1" "RF00003" "HMGB2" "HMGB2" ...

ck <- compareCluster(geneCluster = InputList, fun = GSEA ,TERM2GENE=m_t2g, pvalueCutoff =5, pAdjustMethod = "BH")

Error in compareCluster(geneCluster = InputList, fun = GSEA, TERM2GENE = m_t2g, : No enrichment found in any of gene cluster, please check your input... In addition: There were 15 warnings (use warnings() to see them)

I was wondering if I am using the wrong input type. I am able to get enrichment using enricher, but I want to plot the NES.

Thanks in advance Aish.

[guidohooiveld]

Did you notice this message in the error that was reported:

No enrichment found in any of gene cluster, please check your input...

Please try again by setting pvalueCutoff = 1, and pAdjustMethod = "none".

Also note that you made a type in pvalueCutoff =5 (you used 5 rather than 0.05 I guess...)

Moreover, currently the latest version of clusterProfiler is v4.8.2! To be used with R-4.3.x and Bioconductor release v3.17.