[BioC] Help with HyperGTest
James W. MacDonald
jmacdon at med.umich.edu
Wed Nov 11 19:48:33 CET 2009
Hi Yue,
I see the problem now. The Entrez IDs used by this package are for the
MG1655 substrain rather than the DH10B substrain.
I don't think it would be a trivial exercise to make your own annotation
package - this package is built off the ecoliK12.db0 package that Marc
Carlson creates, so it isn't as simple as using SQLForge to create a new
package. Creating the db0 packages is non-trivial, so there are no
facilities (that I know of) for end users to create one.
I don't know the way around this problem, as I am not familiar with the
different E. coli strains. If there is a one-to-one mapping of genes
between strains then you might be able to map your Entrez Gene IDs to
the MG1655 strain and go from there.
Best,
Jim
Yue, Chen - BMD wrote:
> Hi Jim,
>
> Thanks for your answer. I tried to use your suggestion but it still gave
> me the same error. How can I know what entrez IDs are used by
> "org.Eck12.eg.db"? Is there anyway to make my own annotation package for
> EcK12 substr DH10B? Thanks a lot!
>
> Regards,
> Chen, Yue
>
>
> ------------------------------------------------------------------------
> *From:* James W. MacDonald [mailto:jmacdon at med.umich.edu]
> *Sent:* Tue 11/10/2009 1:19 PM
> *To:* Yue, Chen - BMD
> *Cc:* Marc Carlson; bioconductor at stat.math.ethz.ch
> *Subject:* Re: [BioC] Help with HyperGTest
>
> 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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> > >
> ------------------------------------------------------------------------
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> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
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