[BioC] Help with HyperGTest

[James W. MacDonald]

Most likely those values are read in as numeric, which won't work. You 
need to convert to character, or use

targetid <- scan("targetids.txt","c")

to read in.

Best,

Jim



Yue, Chen - BMD wrote:
> Hi Marc and Jim,
>  
> I'm sorry about the stripped attachment. I listed some targetid and 
> ecoliid I used. Can you take a look? Thanks!
>  
> Regards,
>  
> Chen, Yue
>  
> <<targetids.txt>>
> 6058204
> 6058276
> 6058499
> 6058576
> 6058687
> 6058820
> 6058853
> 6058937
> 6058989
> 6059024
> 6059029
> 6059123
>  
> <<ecoliids.txt>>
> 6061999
> 6061998
> 6061997
> 6061996
> 6061995
> 6061994
> 6061993
> 6061992
> 6061991
> 6061990
> 6061989
> 6061988
> 6061987
> 6061986
> 6061985
> 6061984
> 6061983
> 6061982
> 6061981
> 6061980
> 6061979
> 6061978
> 6061977
> 6061976
> 6061975
> 6061974
> 6061973
> 6061972
> 6061971
> 6061970
> 6061969
> 6061968
> 6061967
>  
> 
> ------------------------------------------------------------------------
> *From:* Marc Carlson [mailto:mcarlson at fhcrc.org]
> *Sent:* Tue 11/10/2009 11:39 AM
> *To:* Yue, Chen - BMD
> *Cc:* bioconductor at stat.math.ethz.ch
> *Subject:* Re: [BioC] Help with HyperGTest
> 
> Hi Yue,
> 
> It's a good idea to always give us the output of sessionInfo() when you
> post, but I can tell you that with this error, the problem is usually
> caused by the input IDs.  If you are using the org.EcK12.eg.db then  you
> must use IDs that are Entrez Gene IDs.  What is the output from
> head(targetids) and head(ecoliids)?
> 
>   Marc
> 
> 
> 
> 
> Yue, Chen - BMD wrote:
>  > Dear All,
>  >
>  > I hope to get some help on the hyperGTest in GOstats. I want to do an 
> GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I 
> attached the target id file, partial ecoli id file (as universeGeneIds) 
> and sessionInfo to the email. The following is my commands and error. It 
> seems that my gene id is not found in the annotation package but I don't 
> know how to find out what gene ids are included in the package. I used 
> "org.EcK12.eg.db" package which uses Entrez ids and my R version is 
> 2.9.2 on WinXP. Should I use a different annotation package? Thank you 
> very much!
>  >
>  >  
>  >> targettable <- read.table("D:/RProjects/targetids.txt")
>  >> ecolitable <- read.table("D:/RProjects/ecoliids.txt")
>  >> targetids <- unique(targettable[,1])
>  >> ecoliids <- unique(ecolitable[,1])
>  >> params = new("GOHyperGParams", geneIds=targetids, 
> universeGeneIds=ecoliids, annotation="org.EcK12.eg.db", ontology="BP", 
> pvalueCutoff=0.01, conditional=FALSE, testDirection="over")
>  >> BPoverTest = hyperGTest(params)
>  >>    
>  > Error in getUniverseHelper(probes, datPkg, entrezIds) :
>  >   After filtering, there are no valid IDs that can be used as the 
> Gene universe.
>  >   Check input values to confirm they are the same type as the central 
> ID used by your annotation package.
>  >   For chip packages, this will still mean the central GENE identifier 
> used by the package (NOT the probe IDs).
>  >
>  > Regards,
>  >
>  > Yue
>  >
>  >
>  >
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