enrichgo clusterProfiler: no results, that's possible?
1
0
Entering edit mode
2.0 years ago
m986 ▴ 10

Hi! I am doing an enrichment analysis using clusterProfiler, with the function: "enrichGO", but in one of my analyzes this does not inform anything enriched, is that possible?

[1] ID Description GeneRatio BgRatio pvalue p.adjust qvalue
[8] geneID Count
<0 rows> (or 0-length row.names)

My geneList has 493 genes, my organism is not a model, another 2 geneList worked perfectly, but this list did not

d<-c(  "107838750","107838884","107839045","107839063","107839107","107839143","107839156",
       "107839392","107839399","107839518","107839591","107839697","107839754","107839798",
       "107839982","107840052","107840083","107840094","107840096","107840155","107840201",
       "107840214","107840217","107840225","107840237","107840426","107840463","107840470",
       "107840525","107840597","107840600","107840615","107840747","107840888","107840934",
       "107840968","107841030","107841033","107841106","107841108","107841134","107841483",
       "107841728","107841877","107841888","107841906","107842013","107842174","107842189",
       "107842218","107842284","107842304","107842344","107842853","107842861","107842951",
       "107842965","107843062","107843087","107843095","107843345","107843348","107843408",
       "107843454","107843465","107843652","107843660","107843680","107843684","107843905",
       "107843938","107844024","107844039","107844040","107844360","107844456","107844515",
       "107844722","107844733","107844746","107844911","107845137","107845267","107845330",
       "107845435","107845475","107845491","107845519","107845656","107845662","107845680",
       "107845694","107845742","107845748","107845758","107845775","107845814","107846116",
       "107846135","107846169","107846472","107846592","107846829","107846860","107846908",
       "107847027","107847527","107847539","107847648","107847783","107847868","107847894",
       "107848014","107848119","107848174","107848249","107848250","107848263","107848328",
       "107848334","107848363","107848409","107848423","107848433","107848464","107848491",
       "107849555","107849641","107849650","107849656","107849659","107849935","107850012",
       "107850273","107850587","107850603","107850630","107850768","107850844","107850869",
       "107850970","107851036","107851087","107851100","107851125","107851188","107851200",
       "107851201","107851216","107851262","107851294","107851336","107851386","107851402",
       "107851417","107851448","107851473","107851611","107851622","107851664","107851791",
       "107851863","107851957","107852043","107852354","107852393","107852453","107852465",
       "107852466","107852529","107852617","107852637","107852645","107852739","107852800",
       "107852809","107852856","107852867","107852871","107852913","107852921","107853007",
       "107853079","107853386","107853713","107853805","107853951","107854097","107854099",
       "107854174","107854221","107854232","107854266","107854410","107854539","107854608",
       "107854628","107854948","107854980","107855122","107855179","107855249","107855270",
       "107855271","107855314","107855327","107855502","107855568","107855591","107855640",
       "107855760","107855779","107855782","107856009","107856092","107856318","107856323",
       "107856349","107856376","107856402","107856415","107856533","107856604","107856682",
       "107857008","107857095","107857116","107857140","107857159","107857219","107857374",
       "107857553","107857663","107858258","107858453","107858499","107858543","107858722",
       "107858844","107858913","107858916","107859092","107859129","107859131","107859310",
       "107859324","107859325","107859367","107859443","107859478","107859507","107859529",
       "107859597","107859727","107859764","107859846","107859851","107860013","107860048",
       "107860049","107860054","107860082","107860203","107860232","107860244","107860341",
       "107860496","107860596","107860782","107861071","107861218","107861335","107861339",
       "107861370","107861404","107861580","107861664","107861673","107861681","107861768",
       "107861794","107861832","107861838","107861872","107861995","107862048","107862241",
       "107862247","107862281","107862341","107862387","107862495","107862609","107862699",
       "107862709","107862766","107862768","107862773","107862787","107862809","107862858",
       "107862886","107862942","107862969","107863135","107863139","107863182","107863408",
       "107863423","107863655","107863783","107863824","107863850","107863973","107864041",
       "107864042","107864058","107864267","107864282","107864325","107864352","107864353",
       "107864418","107864539","107864567","107864568","107864569","107864586","107864637",
       "107864752","107864773","107865421","107865537","107865643","107865660","107865671",
       "107865680","107865691","107865812","107865847","107865999","107866039","107866061",
       "107866154","107866379","107866398","107866649","107866823","107866867","107866953",
       "107867088","107867110","107867184","107867185","107867209","107867212","107867314",
       "107867316","107867326","107867358","107867420","107867422","107867429","107867449",
       "107867489","107867536","107867571","107867576","107867640","107867673","107867678",
       "107867791","107867842","107867971","107868066","107868198","107868255","107868274",
       "107868368","107868464","107869503","107869796","107870048","107870180","107870289",
       "107870408","107870478","107870506","107870524","107870529","107870535","107870735",
       "107871071","107871109","107871171","107871249","107871434","107871527","107872053",
       "107872217","107872236","107872298","107872576","107872675","107872681","107872700",
       "107872785","107872974","107873014","107873019","107873059","107873096","107873354",
       "107873419","107873515","107873719","107873767","107873824","107873869","107873879",
       "107874005","107874242","107874515","107874558","107874649","107874687","107874724",
       "107874905","107874941","107874961","107875026","107875119","107875177","107875210",
       "107875370","107875415","107875536","107875555","107875571","107875616","107875768",
       "107875773","107875794","107875833","107876113","107876253","107876376","107876398",
       "107876798","107876947","107877009","107877011","107877018","107877019","107877220",
       "107877230","107877363","107877439","107877484","107877516","107877517","107877533",
       "107877539","107877542","107877546","107877636","107877669","107877717","107877749",
       "107877868","107877900","107878075","107878179","107878219","107878302","107878318",
       "107878328","107878329","107878499","107878595","107878631","107878756","107878791",
       "107878895","107878982","107879143","107879446","107879447","107879449","107879950",
       "107879994","107879997","107879999")

enrich_T48<-enrichGO(d,OrgDb=orgdb,keyType="ENTREZID",ont="BP", ,qvalueCutoff = 0.05,
                    pAdjustMethod="BH",universe=universeList)

Other geneLists resulted in enrichments using the same variables, and orgdb was made using AnnotationHub with C. annuum Thanks!!!!

clusterProfiler enrichgo go enrichment analysis • 955 views
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0
Entering edit mode
2.0 years ago

Of course it's possible, why wouldn't it be? It's also possible your organism doesn't have many GO annotations, so it may be worth exploring your OrgDb object to see if that is the case.

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