Help with HyperGTest
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@yue-chen-bmd-3790
Last seen 10.3 years ago
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 This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.
Annotation probe GOstats Annotation probe GOstats • 1.7k views
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@yue-chen-bmd-3790
Last seen 10.3 years ago
Dear All, I'm new to Bioconductor, so I apologize if my problem is too naive. I want to do an GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I attached the target id file and ecoli id file (as universeGeneIds) 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. Can someone help me find out what is wrong? 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 This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you.
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
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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 > > > > This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@james-w-macdonald-5106
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Hi Yue, 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). Your error message indicates that the ecoliids are not Entrez Gene IDs. Your attachments were stripped so we can't look at these data, but you can give us an idea by using e.g., head(ecoliids) and supplying us with the output. Best, Jim > > Regards, > > Yue > > > > This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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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@yue-chen-bmd-3790
Last seen 10.3 years ago
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@fhcrc.org] Sent: Tue 11/10/2009 11:39 AM To: Yue, Chen - BMD Cc: bioconductor@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 > > > > This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. [[alternative HTML version deleted]]
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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 > > > > > > > > This email is intended only for the use of the individual or entity > to which it is addressed and may contain information that is privileged > and confidential. If the reader of this email message is not the > intended recipient, you are hereby notified that any dissemination, > distribution, or copying of this communication is prohibited. If you > have received this email in error, please notify the sender and > destroy/delete all copies of the transmittal. Thank you. > > > > > > ----------------------------------------------------------------- ------- > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > This email is intended only for the use of the individ...{{dropped:19}}
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@yue-chen-bmd-3790
Last seen 10.3 years ago
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@med.umich.edu] Sent: Tue 11/10/2009 1:19 PM To: Yue, Chen - BMD Cc: Marc Carlson; bioconductor@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@fhcrc.org] > *Sent:* Tue 11/10/2009 11:39 AM > *To:* Yue, Chen - BMD > *Cc:* bioconductor@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 > > > > > > > > This email is intended only for the use of the individual or entity > to which it is addressed and may contain information that is privileged > and confidential. If the reader of this email message is not the > intended recipient, you are hereby notified that any dissemination, > distribution, or copying of this communication is prohibited. If you > have received this email in error, please notify the sender and > destroy/delete all copies of the transmittal. Thank you. > > > > > > ----------------------------------------------------------------- ------- > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > This email is intended only for the use of the individual or entity to > which it is addressed and may contain information that is privileged and > confidential. If the reader of this email message is not the intended > recipient, you are hereby notified that any dissemination, distribution, > or copying of this communication is prohibited. If you have received > this email in error, please notify the sender and destroy/delete all > copies of the transmittal. Thank you. -- 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 This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. [[alternative HTML version deleted]]
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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 > > > > > > > > > > > > This email is intended only for the use of the individual or entity > > to which it is addressed and may contain information that is privileged > > and confidential. If the reader of this email message is not the > > intended recipient, you are hereby notified that any dissemination, > > distribution, or copying of this communication is prohibited. If you > > have received this email in error, please notify the sender and > > destroy/delete all copies of the transmittal. Thank you. > > > > > > > > > > -------------------------------------------------------------------- ---- > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > This email is intended only for the use of the individual or entity to > > which it is addressed and may contain information that is privileged and > > confidential. If the reader of this email message is not the intended > > recipient, you are hereby notified that any dissemination, distribution, > > or copying of this communication is prohibited. If you have received > > this email in error, please notify the sender and destroy/delete all > > copies of the transmittal. Thank you. > > -- > 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 > > > > > This email is intended only for the use of the individ...{{dropped:19}}
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Hi Yue, I am afraid in that case we don't have an annotation package for you (we only support the most popular strains). But if you want to use GOstats there is STILL a workaround for you if you have access to some raw GO to gene ID mappings. This is not as hopeless as it may sound, you can probably get such data from NCBI or failing that from the blast2GO project. Then you can read the "GOstatsForUnsupportedOrganisms.pdf" vignette in the documentation for the GOstats package. You can find this file here: http://www.bioconductor.org/packages/devel/bioc/html/GOstats.html Please let me know if you have more questions, Marc James W. MacDonald wrote: > 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 >> >> 6058204 >> >> 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 >> > > >> > > >> > > >> > > This email is intended only for the use of the individual or >> entity >> > to which it is addressed and may contain information that is >> privileged >> > and confidential. If the reader of this email message is not the >> > intended recipient, you are hereby notified that any dissemination, >> > distribution, or copying of this communication is prohibited. If you >> > have received this email in error, please notify the sender and >> > destroy/delete all copies of the transmittal. Thank you. >> > > >> > > > > >> ------------------------------------------------------------------- ----- >> > > >> > > _______________________________________________ >> > > Bioconductor mailing list >> > > Bioconductor at stat.math.ethz.ch >> > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > > >> > >> > This email is intended only for the use of the individual or >> entity to >> > which it is addressed and may contain information that is >> privileged and >> > confidential. If the reader of this email message is not the intended >> > recipient, you are hereby notified that any dissemination, >> distribution, >> > or copying of this communication is prohibited. If you have received >> > this email in error, please notify the sender and destroy/delete all >> > copies of the transmittal. Thank you. >> >> -- >> 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 >> >> >> >> >> This email is intended only for the use of the individ...{{dropped:19}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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