Error simplifyGOFromMultipleLists() version 1.8

[IrSoler]

Dear simplifyEnrichment team,

I am trying to use the simplifyGOFromMultipleLists() function of package version 1.8.0, but I get the following error:

Error in apply(mm[index, ], 2, function(x) sum(x >= transform(padj_cutoff))) :
dim(X) must have a positive length

The code I am using is:

terms.A = c("GO:0007409", "GO:0060592", "GO:2000288", "GO:0018401", "GO:0071679", "GO:0021932", "GO:0015918", "GO:0048488", "GO:0060078", "GO:0046777")

terms. B = c("GO:0007409", "GO:0051272", "GO:0051412", "GO:0021762", "GO:2000977", "GO:0014012", "GO:1900242", "GO:0098974", "GO:0001525", "GO:0060052", "GO:0010248", "GO:0048488", "GO:0051092", "GO: 0009409", "GO:0086064", "GO:0051131", "GO:0010894", "GO:0042026", "GO:0007420", "GO:0032092", "GO:0045744", "GO:0071277", "GO:1903416", "GO:0002428", "GO:0048662", "GO:0048167", "GO:0006883", "GO:2000300")

terms = list("terms.A" = terms.A, "terms.B" = terms.B)

s = simplifyGOFromMultipleLists(terms, ont = "BP", db = 'org.Hs.eg.db', measure = "Rel")

However, when I use the same function with the code of version 1.6 (version where barplots cannot be obtained) I don't get any error.

I was wondering if I have misunderstood the usage of this function or if this is a bug to report.

Any help would be appreciated. Thanks you in advance!

Best wishes,
Ir

[Jadziaa]

I am getting the same error with package version 1.9.1.

The code I am using is:

BSvsGS_BSUP =. c("GO:0001709","GO:0001708","GO:0002696","GO:0050877","GO:0009606","GO:0010753","GO:0043577","GO:0051343","GO:1902159","GO:1902160","GO:0040012","GO:0061062","GO:0019932","GO:0050918","GO:0042593","GO:0040011","GO:0035112","GO:0018196","GO:0018279","GO:0071887","GO:0006925","GO:0050864","GO:0071888","GO:0008284","GO:0097305","GO:2000106","GO:0033500","GO:0033273")

LSvsGS_LSUP = c("GO:0006925","GO:0071888","GO:0033273","GO:0032944","GO:0070663","GO:0009100","GO:0040011","GO:0046323","GO:0046324","GO:0097305","GO:0071887","GO:2000107","GO:0040013","GO:0010827","GO:0032943","GO:0070661","GO:1904659","GO:0008645","GO:0015749","GO:0034219","GO:0005975","GO:0008643","GO:0009636")

my_list = list("BSvsGS_BSUP" = BSvsGS_BSUP, "LSvsGS_LSUP" = LSvsGS_LSUP)

s = simplifyGOFromMultipleLists(my_list, ont = "BP")

The error message after running for a while:

Error in apply(mm[index, ], 2, function(x) sum(x >= transform(padj_cutoff))) :
dim(X) must have a positive length

When I am trying with the test data everything works fine.

[L-Yuyang]

I tried to solve it by lowering the threshold of padj_cutoff. Perhaps the default threshold is too high, causing some lists to become empty after filtering.