GO term not found error, Yeast data, gseGO test about clusterprofiler HOT 7 CLOSED

Hi Dean,

Can you give me some sample IDs that can replicate this issue?

from clusterprofiler.

Hi Guangchuang,

Table$IDs are in the attached .txt file.

Regards,

Dean

From: Guangchuang Yu [mailto:[email protected]]
Sent: 15 June 2015 13:55
To: GuangchuangYu/clusterProfiler
Cc: Hammond, Dean
Subject: Re: [clusterProfiler] GO term not found error, Yeast data, gseGO test (#12)

Hi Dean,

Can you give me some sample IDs that can replicate this issue?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/12#issuecomment-112058195.

YCL057C-A
YCL057W
YCL043C
YCL040W
YCL025C
YCL018W
YCL017C
YCL011C
YCL009C
YCL001W
YCR002C
YCR003W
YCR004C
YCR009C
YCR012W
YCR028C-A
YCR046C
YCR051W
YCR053W
YCR072C
YCR084C
YCR086W
YCR088W
YCR090C
YCR093W
YCR105W
YFL053W
YFL045C
YFL039C
YFL038C
YFL037W
YFL036W
YFL034C-A
YFL030W
YFL028C
YFL022C
YFL018C
YFL016C
YFL014W
YFL010C
YFL005W
YFR001W
YFR004W
YFR006W
YFR009W
YFR010W
YFR011C
YFR015C
YFR016C
YFR031C-A
YFR033C
YFR037C
YFR044C
YFR047C
YFR049W
YFR050C
YFR051C
YFR052W
YLL029W
YLL026W
YLL024C
YLL018C
YLL011W
YLL008W
YLL050C
YLL045C
YLL041C
YLR008C
YLR009W
YLR017W
YLR022C
YLR023C
YLR027C
YLR038C
YLR043C
YLR044C
YLR058C
YLR059C
YLR060W
YLR069C
YLR074C
YLR075W
YLR081W
YLR083C
YLR109W
YLR120C
YLR150W
YLR153C
YLR167W
YLR172C
YLR174W
YLR175W
YLR178C
YLR186W
YLR192C
YLR195C
YLR196W
YLR197W
YLR208W
YLR216C
YLR220W
YLR229C
YLR249W
YLR259C
YLR264W
YLR286C
YLR291C
YLR293C
YLR295C
YLR303W
YLR304C
YLR312W-A
YLR314C
YLR325C
YLR328W
YLR333C
YLR335W
YLR340W
YLR347C
YLR348C
YLR354C
YLR355C
YLR359W
YLR378C
YLR388W
YLR401C
YLR406C
YLR409C
YLR420W
YLR421C
YLR429W
YLR435W
YLR438W
YLR439W
YLR447C
YLR448W
YAL039C
YAL038W
YAL036C
YAL035W
YAL025C
YAL023C
YAL016W
YAL012W
YAL062W
YAL060W
YAL059W
YAL054C
YAL049C
YAL044C
YAL003W
YAR007C
YAR015W
YDL215C
YDL212W
YDL208W
YDL202W
YDL198C
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YDL192W
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YDL185W
YDL181W
YDL246C
YDL225W
YDL178W
YDL171C
YDL168W
YDL166C
YDL165W
YDL160C
YDL145C
YDL143W
YDL140C
YDL137W
YDL135C
YDL132W
YDL131W
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YDL126C
YDL125C
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YDL103C
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YDL097C
YDL095W
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YDL078C
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YDL067C
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YDL060W
YDL055C
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YDL040C
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YDL018C
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YDR019C
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YDR025W
YDR032C
YDR035W
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YDR039C
YDR041W
YDR044W
YDR050C
YDR060W
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YDR087C
YDR091C
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YDR109C
YDR115W
YDR116C
YDR121W
YDR127W
YDR129C
YDR135C
YDR148C
YDR155C
YDR158W
YDR161W
YDR165W
YDR168W
YDR172W
YDR174W
YDR175C
YDR177W
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YDR190C
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YDR212W
YDR214W
YDR224C
YDR226W
YDR232W
YDR233C
YDR236C
YDR237W
YDR238C
YDR256C
YDR257C
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YDR304C
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YDR322C-A
YDR324C
YDR328C
YDR337W
YDR339C
YDR341C
YDR343C
YDR346C
YDR347W
YDR353W
YDR354W
YDR363W-A
YDR372C
YDR375C
YDR377W
YDR378C
YDR381W
YDR382W
YDR388W
YDR394W
YDR398W
YDR399W
YDR405W
YDR408C
YDR427W
YDR429C
YDR432W
YDR447C
YDR454C
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YDR487C
YDR493W
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YBL039C
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YBR011C
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YBR080C
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YBR084C-A
YBR086C
YBR088C
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YBR115C
YBR118W
YBR121C
YBR122C
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YBR143C
YBR146W
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YBR159W
YBR160W
YBR171W
YBR172C
YBR185C
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YBR196C
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YBR221C
YBR247C
YBR249C
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YBR267W
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YBR283C
YBR286W
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YGL253W
YGL246C
YGL225W
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YGL210W
YGL207W
YGL206C
YGL205W
YGL202W
YGL200C
YGL195W
YGL191W
YGL189C
YGL187C
YGL173C
YGL148W
YGL137W
YGL129C
YGL123W
YGL120C
YGL115W
YGL111W
YGL106W
YGL105W
YGL103W
YGL099W
YGL078C
YGL076C
YGL070C
YGL068W
YGL064C
YGL055W
YGL048C
YGL044C
YGL043W
YGL040C
YGL031C
YGL030W
YGL026C
YGL011C
YGL009C
YGL008C
YGR012W
YGR019W
YGR020C
YGR032W
YGR034W
YGR037C
YGR054W
YGR061C
YGR063C
YGR076C
YGR078C
YGR082W
YGR083C
YGR085C
YGR086C
YGR090W
YGR094W
YGR103W
YGR124W
YGR128C
YGR130C
YGR132C
YGR135W
YGR152C
YGR155W
YGR159C
YGR162W
YGR165W
YGR167W
YGR173W
YGR181W
YGR183C
YGR185C
YGR187C
YGR192C
YGR193C
YGR207C
YGR209C
YGR210C
YGR211W
YGR214W
YGR215W
YGR218W
YGR220C
YGR229C
YGR231C
YGR234W
YGR235C
YGR240C
YGR243W
YGR244C
YGR245C
YGR253C
YGR254W
YGR255C
YGR264C
YGR266W
YGR271C-A
YGR282C
YGR285C
YJL200C
YJL191W
YJL190C
YJL180C
YJL177W
YJL174W
YJL167W
YJL166W
YJL156C
YJL153C
YJL140W
YJL138C
YJL136C
YJL130C
YJL124C
YJL111W
YJL096W
YJL080C
YJL068C
YJL063C
YJL041W
YJL034W
YJL033W
YJL026W
YJL014W
YJL008C
YJL002C
YJL001W
YJR007W
YJR010W
YJR014W
YJR016C
YJR017C
YJR019C
YJR045C
YJR048W
YJR051W
YJR064W
YJR065C
YJR070C
YJR074W
YJR075W
YJR076C
YJR077C
YJR096W
YJR101W
YJR104C
YJR105W
YJR113C
YJR117W
YJR121W
YJR123W
YJR125C
YJR139C
YJR145C
YJR148W
YKL196C
YKL195W
YKL192C
YKL190W
YKL182W
YKL216W
YKL213C
YKL211C
YKL210W
YKL172W
YKL167C
YKL157W
YKL152C
YKL150W
YKL148C
YKL145W
YKL142W
YKL138C
YKL137W
YKL128C
YKL122C
YKL117W
YKL106W
YKL104C
YKL103C
YKL085W
YKL081W
YKL073W
YKL067W
YKL065C
YKL060C
YKL056C
YKL054C
YKL046C
YKL035W
YKL024C
YKL021C
YKL016C
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YKL001C
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YKR009C
YKR014C
YKR016W
YKR026C
YKR043C
YKR048C
YKR065C
YKR066C
YKR070W
YKR076W
YKR080W
YKR081C
YKR092C
YKR094C
YKR097W
YOL127W
YOL126C
YOL123W
YOL151W
YOL143C
YOL142W
YOL139C
YOL121C
YOL120C
YOL111C
YOL097C
YOL094C
YOL086C
YOL084W
YOL077W-A
YOL077C
YOL071W
YOL064C
YOL057W
YOL049W
YOL041C
YOL040C
YOL039W
YOL038W
YOL031C
YOL030W
YOL016C
YOL012C
YOL007C
YOL006C
YOL005C
YOR007C
YOR020C
YOR027W
YOR042W
YOR046C
YOR051C
YOR056C
YOR061W
YOR063W
YOR065W
YOR091W
YOR094W
YOR096W
YOR099W
YOR100C
YOR101W
YOR110W
YOR117W
YOR120W
YOR122C
YOR128C
YOR133W
YOR136W
YOR142W
YOR150W
YOR151C
YOR153W
YOR158W
YOR164C
YOR168W
YOR176W
YOR184W
YOR187W
YOR198C
YOR201C
YOR204W
YOR206W
YOR209C
YOR224C
YOR232W
YOR254C
YOR259C
YOR261C
YOR270C
YOR272W
YOR276W
YOR281C
YOR286W
YOR293W
YOR294W
YOR298C-A
YOR310C
YOR312C
YOR323C
YOR326W
YOR327C
YOR332W
YOR335C
YOR341W
YOR361C
YOR362C
YOR369C
YOR388C
Q0045
Q0250
YIL155C
YIL142W
YIL136W
YIL133C
YIL125W
YIL118W
YIL116W
YIL109C
YIL094C
YIL093C
YIL087C
YIL078W
YIL076W
YIL075C
YIL070C
YIL069C
YIL062C
YIL053W
YIL052C
YIL051C
YIL043C
YIL041W
YIL035C
YIL033C
YIL022W
YIL021W
YIR001C
YIR012W
YIR034C
YIR035C
YIR037W
YIR038C
YML106W
YML105C
YML094W
YML092C
YML086C
YML085C
YML081C-A
YML078W
YML074C
YML072C
YML128C
YML126C
YML123C
YML069W
YML063W
YML056C
YML055W
YML052W
YML042W
YML028W
YML026C
YML025C
YML022W
YML014W
YML012W
YML008C
YML004C
YMR012W
YMR015C
YMR024W
YMR027W
YMR031C
YMR038C
YMR039C
YMR049C
YMR058W
YMR074C
YMR079W
YMR083W
YMR089C
YMR090W
YMR092C
YMR093W
YMR096W
YMR099C
YMR105C
YMR108W
YMR116C
YMR118C
YMR120C
YMR121C
YMR131C
YMR143W
YMR145C
YMR146C
YMR149W
YMR158W
YMR173W
YMR183C
YMR186W
YMR188C
YMR189W
YMR193W
YMR194W
YMR196W
YMR203W
YMR205C
YMR217W
YMR225C
YMR226C
YMR228W
YMR229C
YMR234W
YMR235C
YMR237W
YMR244C-A
YMR246W
YMR250W
YMR260C
YMR272C
YMR276W
YMR286W
YMR290C
YMR300C
YMR303C
YMR305C
YMR307W
YMR308C
YMR309C
YMR310C
YMR314W
YNL315C
YNL312W
YNL306W
YNL290W
YNL287W
YNL284C
YNL281W
YNL265C
YNL255C
YNL252C
YNL251C
YNL248C
YNL247W
YNL244C
YNL241C
YNL220W
YNL212W
YNL209W
YNL208W
YNL189W
YNL185C
YNL182C
YNL178W
YNL177C
YNL175C
YNL173C
YNL162W
YNL153C
YNL147W
YNL137C
YNL135C
YNL134C
YNL132W
YNL131W
YNL123W
YNL121C
YNL117W
YNL112W
YNL111C
YNL110C
YNL104C
YNL081C
YNL079C
YNL075W
YNL071W
YNL067W
YNL064C
YNL061W
YNL055C
YNL052W
YNL045W
YNL044W
YNL037C
YNL036W
YNL035C
YNL031C
YNL030W
YNL010W
YNL007C
YNL005C
YNL002C
YNR001C
YNR016C
YNR017W
YNR018W
YNR021W
YNR022C
YNR030W
YNR034W
YNR035C
YNR037C
YNR043W
YNR046W
YNR050C
YNR051C
YNR053C
YPL243W
YPL239W
YPL237W
YPL235W
YPL231W
YPL273W
YPL262W
YPL226W
YPL225W
YPL220W
YPL218W
YPL215W
YPL212C
YPL211W
YPL210C
YPL184C
YPL179W
YPL173W
YPL171C
YPL170W
YPL160W
YPL154C
YPL146C
YPL145C
YPL143W
YPL135W
YPL132W
YPL131W
YPL129W
YPL127C
YPL126W
YPL118W
YPL117C
YPL113C
YPL111W
YPL106C
YPL094C
YPL093W
YPL091W
YPL090C
YPL088W
YPL082C
YPL078C
YPL063W
YPL059W
YPL048W
YPL043W
YPL037C
YPL031C
YPL028W
YPL013C
YPL012W
YPL010W
YPL008W
YPL004C
YPR004C
YPR010C
YPR016C
YPR020W
YPR024W
YPR028W
YPR033C
YPR035W
YPR036W
YPR041W
YPR043W
YPR052C
YPR069C
YPR074C
YPR080W
YPR098C
YPR100W
YPR103W
YPR108W
YPR110C
YPR127W
YPR129W
YPR132W
YPR137W
YPR140W
YPR144C
YPR149W
YPR160W
YPR163C
YPR165W
YPR166C
YPR181C
YPR183W
YPR187W
YPR191W
YHL034C
YHL015W
YHL013C
YHL011C
YHL004W
YHL001W
YHR001W-A
YHR005C-A
YHR007C
YHR008C
YHR010W
YHR013C
YHR019C
YHR020W
YHR021C
YHR025W
YHR027C
YHR037W
YHR038W
YHR039C-A
YHR042W
YHR049W
YHR051W
YHR052W
YHR059W
YHR064C
YHR068W
YHR072W-A
YHR074W
YHR087W
YHR089C
YHR104W
YHR107C
YHR110W
YHR112C
YHR113W
YHR116W
YHR128W
YHR138C
YHR147C
YHR163W
YHR169W
YHR170W
YHR179W
YHR183W
YHR187W
YHR190W
YHR193C
YHR196W
YHR200W
YHR211W
YEL058W
YEL056W
YEL054C
YEL046C
YEL042W
YEL040W
YEL037C
YEL034W
YEL031W
YEL026W
YEL024W
YEL020W-A
YEL017W
YEL013W
YEL003W
YEL002C
YEL001C
YER002W
YER003C
YER004W
YER006W
YER009W
YER012W
YER019C-A
YER021W
YER023W
YER025W
YER027C
YER029C
YER036C
YER042W
YER043C
YER044C
YER050C
YER055C
YER063W
YER065C
YER069W
YER070W
YER073W
YER074W-A
YER080W
YER081W
YER086W
YER089C
YER090W
YER091C
YER094C
YER102W
YER103W
YER110C
YER112W
YER117W
YER120W
YER122C
YER133W
YER136W
YER143W
YER145C
YER154W
YER156C
YER159C
YER165W
YER168C
YER178W
YGR169C-A

from clusterprofiler.

thanks for your report.

Yes, it's due to deprecated GO term.

This issue had been removed in clusterProfiler version >=2.2.3

BTW: I also detect wrong usage in your command:

ego2 <- gseGO(geneList = Table$IDs, organism = "yeast", ont = "MF",
nPerm = 100, minGSSize = 120, pvalueCutoff = 0.01, verbose = FALSE)

geneList should not be a vector of gene IDs, but a vector of order numerical number (eg fold change, pvalues) and named by corresponding gene IDs.

from clusterprofiler.

OK. Thanks! That's great. Thanks for correcting the code too.....!

from clusterprofiler.

Hi,

Clusterprofiler would not update unless I use the devel=TRUE in biocLite. I have done this but still get the same error when I try the ego2 test (with the correct geneList!).
I also see the following when loading clusterProfiler:

library(clusterProfiler)
Loading required package: DBI

Warning message:
replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

Any ideas? Sorry to bother you about this!

Regards,

Dean

from clusterprofiler.

You should wait 2-3 days for Bioconductor to update tallbar.

Don't mixed release and devel versions of Bioconductor packages. That may introduce a lot of issues.

from clusterprofiler.

OK. Thanks Guangchuang.

From: Guangchuang Yu [mailto:[email protected]]
Sent: 17 June 2015 12:52
To: GuangchuangYu/clusterProfiler
Cc: Hammond, Dean
Subject: Re: [clusterProfiler] GO term not found error, Yeast data, gseGO test (#12)

You should wait 2-3 days for Bioconductor to update tallbar.

Don't mixed release and devel versions of Bioconductor packages. That may introduce a lot of issues.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/12#issuecomment-112768702.

from clusterprofiler.