GOstats: get genes for correspond� ing enriched GO term
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Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? best, Tim -- output of sessionInfo(): Thanks for any comments. -- Sent via the guest posting facility at bioconductor.org.
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Would "probeSetSummary()" do what your want? Yuan On 21 Jul 2012, at 02:47, Tim [guest] wrote: > > Hi, > > I used GOstats to perform enrichment test on a set of genes (20). > > There are 7 GO terms with pvalue less than cuttoff and therefore > shown in the result table. > > How can I get the information that which gene in the input gene set > belong to which GO term of these enriched GO terms? > > > > > best, > > Tim > > -- output of sessionInfo(): > > Thanks for any comments. > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, Yuan Thanks alot for your help. I used yeast ORF id as input vectors of geneIds and universeGeneIds. These are the summary of GOHyperGResult instance Gene to GO BP test for over-representation 1660 GO BP ids tested (9 have p < 0.01) Selected gene set size: 427 Gene universe size: 5616 Annotation package: org.Sc.sgd when I used ps<-probeSetSummary(over,0.05) I got warning: The vector of geneIds used to create the GOHyperGParamsobject was not a named vector. If you want to know theprobesets that contributed to this result either usea named vector for geneIds, or pass a vector of probeset IDs via sigProbesets. when I use the input geneIDs (segene) to pass the vector via sgProbesets like: ps<-probeSetSummary(over,0.05,,segene) //segene is input yeast ORF ID I still got a empty resut. Did I do something wrong? Thanks for further help. Tim On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao <yuan.x.hao@gmail.com> wrote: > > Would "probeSetSummary()" do what your want? > > Yuan > > > On 21 Jul 2012, at 02:47, Tim [guest] wrote: > > >> Hi, >> >> I used GOstats to perform enrichment test on a set of genes (20). >> >> There are 7 GO terms with pvalue less than cuttoff and therefore shown in >> the result table. >> >> How can I get the information that which gene in the input gene set >> belong to which GO term of these enriched GO terms? >> >> >> >> >> best, >> >> Tim >> >> -- output of sessionInfo(): >> Thanks for any comments. >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]]
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Hi Tim, On 7/21/2012 10:25 AM, Lan Sky wrote: > Hi, Yuan > Thanks alot for your help. > I used yeast ORF id as input vectors of geneIds and universeGeneIds. > These are the summary of GOHyperGResult instance > > Gene to GO BP test for over-representation > 1660 GO BP ids tested (9 have p< 0.01) > Selected gene set size: 427 > Gene universe size: 5616 > Annotation package: org.Sc.sgd > > when I used > > ps<-probeSetSummary(over,0.05) > > I got warning: > The vector of geneIds used to create the GOHyperGParamsobject was not a > named vector. > If you want to know theprobesets that contributed to this result > either usea named vector for geneIds, or pass a vector of probeset IDs > via sigProbesets. > when I use the input geneIDs (segene) to pass the vector via sgProbesets > like: > > ps<-probeSetSummary(over,0.05,,segene) //segene is input yeast ORF ID > > I still got a empty resut. > Did I do something wrong? Well if you actually used the code above, I am surprised it even ran. Double commas usually result in an error. Also, please re-read the message you got from probeSetSummary(). You are supposed to be passing in a vector of probeset IDs, not re-sending the ORF IDs. Best, Jim > > Thanks for further help. > > Tim > > > > > > > > On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao at="" gmail.com=""> wrote: > >> Would "probeSetSummary()" do what your want? >> >> Yuan >> >> >> On 21 Jul 2012, at 02:47, Tim [guest] wrote: >> >> >>> Hi, >>> >>> I used GOstats to perform enrichment test on a set of genes (20). >>> >>> There are 7 GO terms with pvalue less than cuttoff and therefore shown in >>> the result table. >>> >>> How can I get the information that which gene in the input gene set >>> belong to which GO term of these enriched GO terms? >>> >>> >>> >>> >>> best, >>> >>> Tim >>> >>> -- output of sessionInfo(): >>> Thanks for any comments. >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi, Jim Thanks for your information. I actually don't have any probesetID. I only used yeast ORF id to perform the GO. Do I need to do some mapping from ORF to probeset? In the message I got, it says, "If you want to know theprobesets that contributed to this result either usea named vector for geneIds, or pass a vector of probeset IDs via sigProbesets." "either use a named vector for geneIds." what is that supposed to be the input? Dose it mean geneId instead of probeset? Thanks, Tim On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Tim, > > > On 7/21/2012 10:25 AM, Lan Sky wrote: > >> Hi, Yuan >> Thanks alot for your help. >> I used yeast ORF id as input vectors of geneIds and universeGeneIds. >> These are the summary of GOHyperGResult instance >> >> Gene to GO BP test for over-representation >> 1660 GO BP ids tested (9 have p< 0.01) >> Selected gene set size: 427 >> Gene universe size: 5616 >> Annotation package: org.Sc.sgd >> >> when I used >> >> ps<-probeSetSummary(over,0.05) >> >> I got warning: >> The vector of geneIds used to create the GOHyperGParamsobject was not a >> named vector. >> If you want to know theprobesets that contributed to this result >> either usea named vector for geneIds, or pass a vector of probeset IDs >> via sigProbesets. >> when I use the input geneIDs (segene) to pass the vector via sgProbesets >> like: >> >> ps<-probeSetSummary(over,0.05,**,segene) //segene is input yeast ORF ID >> >> I still got a empty resut. >> Did I do something wrong? >> > > Well if you actually used the code above, I am surprised it even ran. > Double commas usually result in an error. > > Also, please re-read the message you got from probeSetSummary(). You are > supposed to be passing in a vector of probeset IDs, not re-sending the ORF > IDs. > > Best, > > Jim > > > >> Thanks for further help. >> >> Tim >> >> >> >> >> >> >> >> On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao@gmail.com> wrote: >> >> Would "probeSetSummary()" do what your want? >>> >>> Yuan >>> >>> >>> On 21 Jul 2012, at 02:47, Tim [guest] wrote: >>> >>> >>> Hi, >>>> >>>> I used GOstats to perform enrichment test on a set of genes (20). >>>> >>>> There are 7 GO terms with pvalue less than cuttoff and therefore shown >>>> in >>>> the result table. >>>> >>>> How can I get the information that which gene in the input gene set >>>> belong to which GO term of these enriched GO terms? >>>> >>>> >>>> >>>> >>>> best, >>>> >>>> Tim >>>> >>>> -- output of sessionInfo(): >>>> Thanks for any comments. >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> ______________________________****_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/****listinfo/bioconductor<https: st="" at.ethz.ch="" mailman="" **listinfo="" bioconductor=""> >>>> <https: **="" stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> > >>>> Search the archives: http://news.gmane.org/gmane.** >>>> science.biology.informatics.****conductor<http: news.gmane.**="">>>> org/gmane.science.biology.**informatics.conductor<http: news.gma="" ne.org="" gmane.science.biology.informatics.conductor=""> >>>> > >>>> >>>> >>> [[alternative HTML version deleted]] >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
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On 7/21/2012 9:43 PM, Lan Sky wrote: > Hi, Jim > Thanks for your information. > I actually don't have any probesetID. > I only used yeast ORF id to perform the GO. > Do I need to do some mapping from ORF to probeset? > In the message I got, it says, "If you want to know theprobesets that > contributed to this result > either usea named vector for geneIds, or pass a vector of probeset IDs > via sigProbesets." > "either use a named vector for geneIds." > what is that supposed to be the input? > > Dose it mean geneId instead of probeset? It depends on how you did things. You have been pretty cryptic about what you have done, so we have to read between the lines. In general, people use microarray data to do GO analyses. In which case the genes are interrogated by one or more 'reporter' molecules, which if the manufacturer is Affymetrix, are called probesets. When you have a significant GO term, one might want to know which of the significant reporter molecules contributed to that result. So in the case of an Affy analysis, you would pass in a vector of probeset IDs. So if you don't have Affy data, then I assume you have some other manufacturer IDs you could use. Perhaps you could feed in gene IDs, but that wasn't the original intent, and may not work. Best, Jim > Thanks, > Tim > On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Tim, > > > On 7/21/2012 10:25 AM, Lan Sky wrote: > > Hi, Yuan > Thanks alot for your help. > I used yeast ORF id as input vectors of geneIds and > universeGeneIds. > These are the summary of GOHyperGResult instance > > Gene to GO BP test for over-representation > 1660 GO BP ids tested (9 have p< 0.01) > Selected gene set size: 427 > Gene universe size: 5616 > Annotation package: org.Sc.sgd > > when I used > > ps<-probeSetSummary(over,0.05) > > I got warning: > The vector of geneIds used to create the GOHyperGParamsobject > was not a > named vector. > If you want to know theprobesets that contributed to this result > either usea named vector for geneIds, or pass a vector of > probeset IDs > via sigProbesets. > when I use the input geneIDs (segene) to pass the vector via > sgProbesets > like: > > ps<-probeSetSummary(over,0.05,,segene) //segene is input > yeast ORF ID > > I still got a empty resut. > Did I do something wrong? > > > Well if you actually used the code above, I am surprised it even > ran. Double commas usually result in an error. > > Also, please re-read the message you got from probeSetSummary(). > You are supposed to be passing in a vector of probeset IDs, not > re-sending the ORF IDs. > > Best, > > Jim > > > > Thanks for further help. > > Tim > > > > > > > > On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao at="" gmail.com=""> <mailto:yuan.x.hao at="" gmail.com="">> wrote: > > Would "probeSetSummary()" do what your want? > > Yuan > > > On 21 Jul 2012, at 02:47, Tim [guest] wrote: > > > Hi, > > I used GOstats to perform enrichment test on a set of > genes (20). > > There are 7 GO terms with pvalue less than cuttoff and > therefore shown in > the result table. > > How can I get the information that which gene in the > input gene set > belong to which GO term of these enriched GO terms? > > > > > best, > > Tim > > -- output of sessionInfo(): > Thanks for any comments. > > -- > Sent via the guest posting facility at > bioconductor.org <http: bioconductor.org="">. > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/**listinfo/bioconductor <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.="" gmane.org="" gmane.science.biology.informatics.conductor=""> > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > 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 > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi, Jim Sorry for not including enough information. What I have done is simple: Firs, I used most of yeast genome (ORF gene id) as universeGeneIds like: YAL001C YAL002W YAL003W YAL004W YAL005C YAL007C YAL008W YAL009W ... (size 5616) then I used a shorter list of genes as geneIds like: YAL022C YAL023C YAL024C YAL025C YAL026C YAL027W YAL028W YAL029C ... (size 500) then I performed the test. (I think I did reasonably because GOstats can perform test on geneid instead of probesetid, as they describe "If you are using the YEAST annotation package, the vector will consist of yeast systematic names.") then I got result : Gene to GO BP test for over-representation 1660 GO BP ids tested (9 have p< 0.01) Selected gene set size: 427 Gene universe size: 5616 Annotation package: org.Sc.sgd What I need to next is to try get which geneids (represnted in ORF yeast systematic names ) contribute to which enriched GO term (p<0.01). I don't guess that it should necessarily be in probesetid since all inputs are in ORF/ yeast systematic names and not from any microarray data. Many thanks for your help, Tian On Sat, Jul 21, 2012 at 9:37 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > > > On 7/21/2012 9:43 PM, Lan Sky wrote: > >> Hi, Jim >> Thanks for your information. >> I actually don't have any probesetID. >> I only used yeast ORF id to perform the GO. >> Do I need to do some mapping from ORF to probeset? >> In the message I got, it says, "If you want to know theprobesets that >> contributed to this result >> either usea named vector for geneIds, or pass a vector of probeset IDs >> via sigProbesets." >> "either use a named vector for geneIds." >> what is that supposed to be the input? >> >> Dose it mean geneId instead of probeset? >> > > It depends on how you did things. You have been pretty cryptic about what > you have done, so we have to read between the lines. In general, people use > microarray data to do GO analyses. In which case the genes are interrogated > by one or more 'reporter' molecules, which if the manufacturer is > Affymetrix, are called probesets. > > When you have a significant GO term, one might want to know which of the > significant reporter molecules contributed to that result. So in the case > of an Affy analysis, you would pass in a vector of probeset IDs. So if you > don't have Affy data, then I assume you have some other manufacturer IDs > you could use. Perhaps you could feed in gene IDs, but that wasn't the > original intent, and may not work. > > Best, > > Jim > > > Thanks, >> Tim >> >> On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> Hi Tim, >> >> >> On 7/21/2012 10:25 AM, Lan Sky wrote: >> >> Hi, Yuan >> Thanks alot for your help. >> I used yeast ORF id as input vectors of geneIds and >> universeGeneIds. >> These are the summary of GOHyperGResult instance >> >> Gene to GO BP test for over-representation >> 1660 GO BP ids tested (9 have p< 0.01) >> Selected gene set size: 427 >> Gene universe size: 5616 >> Annotation package: org.Sc.sgd >> >> when I used >> >> ps<-probeSetSummary(over,0.05) >> >> I got warning: >> The vector of geneIds used to create the GOHyperGParamsobject >> was not a >> named vector. >> If you want to know theprobesets that contributed to this result >> either usea named vector for geneIds, or pass a vector of >> probeset IDs >> via sigProbesets. >> when I use the input geneIDs (segene) to pass the vector via >> sgProbesets >> like: >> >> ps<-probeSetSummary(over,0.05,**,segene) //segene is input >> yeast ORF ID >> >> I still got a empty resut. >> Did I do something wrong? >> >> >> Well if you actually used the code above, I am surprised it even >> ran. Double commas usually result in an error. >> >> Also, please re-read the message you got from probeSetSummary(). >> You are supposed to be passing in a vector of probeset IDs, not >> re-sending the ORF IDs. >> >> Best, >> >> Jim >> >> >> >> Thanks for further help. >> >> Tim >> >> >> >> >> >> >> >> On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao@gmail.com>> <mailto:yuan.x.hao@gmail.com>> wrote: >> >> >> Would "probeSetSummary()" do what your want? >> >> Yuan >> >> >> On 21 Jul 2012, at 02:47, Tim [guest] wrote: >> >> >> Hi, >> >> I used GOstats to perform enrichment test on a set of >> genes (20). >> >> There are 7 GO terms with pvalue less than cuttoff and >> therefore shown in >> the result table. >> >> How can I get the information that which gene in the >> input gene set >> belong to which GO term of these enriched GO terms? >> >> >> >> >> best, >> >> Tim >> >> -- output of sessionInfo(): >> Thanks for any comments. >> >> -- >> Sent via the guest posting facility at >> bioconductor.org <http: bioconductor.org="">. >> >> >> ______________________________****_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/****listinfo/bioconduc tor<https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor=""> >> <https: **="" stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.****conductor< >> http://news.gmane.**org/gmane.science.biology.**informatics.conduct or<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> > >> >> >> [[alternative HTML version deleted]] >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
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I was wondering how to extract feature importance contributing to a given classifier. e.g. class_lda <- classification(X = khanX, y=khanY, learningsets = fiveCV5iter, classifier = ldaCMA, genesel= genesel_da, nbgene = 10) I would like to get a list of features (probesets) and associated importance contributing to class_lda (Some will have 0 importance??). Is there a way to do this? Thanks in advance. So. > Date: Sat, 21 Jul 2012 22:22:54 -0500 > From: xiaskyer@gmail.com > To: jmacdon@uw.edu > CC: maintainer@bioconductor.org; bioconductor@r-project.org > Subject: Re: [BioC] GOstats: get genes for correspondâ ing enriched GO term > > Hi, Jim > Sorry for not including enough information. > What I have done is simple: > > Firs, I used most of yeast genome (ORF gene id) as universeGeneIds > like: > YAL001C > YAL002W > YAL003W > YAL004W > YAL005C > YAL007C > YAL008W > YAL009W > ... > (size 5616) > > > then I used a shorter list of genes as geneIds like: > YAL022C > YAL023C > YAL024C > YAL025C > YAL026C > YAL027W > YAL028W > YAL029C > ... > (size 500) > > then I performed the test. (I think I did reasonably because GOstats can > perform test on geneid instead of probesetid, as they describe "If you are > using the YEAST annotation package, the vector will consist of yeast > systematic names.") > > then I got result : > Gene to GO BP test for over-representation > 1660 GO BP ids tested (9 have p< 0.01) > Selected gene set size: 427 > Gene universe size: 5616 > Annotation package: org.Sc.sgd > What I need to next is to try get which geneids (represnted in ORF yeast > systematic names ) contribute to which enriched GO term (p<0.01). > I don't guess that it should necessarily be in probesetid since all inputs > are in ORF/ yeast systematic names and not from any microarray data. > > > Many thanks for your help, > > Tian > > > > > > On Sat, Jul 21, 2012 at 9:37 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > > > > > > > On 7/21/2012 9:43 PM, Lan Sky wrote: > > > >> Hi, Jim > >> Thanks for your information. > >> I actually don't have any probesetID. > >> I only used yeast ORF id to perform the GO. > >> Do I need to do some mapping from ORF to probeset? > >> In the message I got, it says, "If you want to know theprobesets that > >> contributed to this result > >> either usea named vector for geneIds, or pass a vector of probeset IDs > >> via sigProbesets." > >> "either use a named vector for geneIds." > >> what is that supposed to be the input? > >> > >> Dose it mean geneId instead of probeset? > >> > > > > It depends on how you did things. You have been pretty cryptic about what > > you have done, so we have to read between the lines. In general, people use > > microarray data to do GO analyses. In which case the genes are interrogated > > by one or more 'reporter' molecules, which if the manufacturer is > > Affymetrix, are called probesets. > > > > When you have a significant GO term, one might want to know which of the > > significant reporter molecules contributed to that result. So in the case > > of an Affy analysis, you would pass in a vector of probeset IDs. So if you > > don't have Affy data, then I assume you have some other manufacturer IDs > > you could use. Perhaps you could feed in gene IDs, but that wasn't the > > original intent, and may not work. > > > > Best, > > > > Jim > > > > > > Thanks, > >> Tim > >> > >> On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon@uw.edu<mailto:> >> jmacdon@uw.edu>> wrote: > >> > >> Hi Tim, > >> > >> > >> On 7/21/2012 10:25 AM, Lan Sky wrote: > >> > >> Hi, Yuan > >> Thanks alot for your help. > >> I used yeast ORF id as input vectors of geneIds and > >> universeGeneIds. > >> These are the summary of GOHyperGResult instance > >> > >> Gene to GO BP test for over-representation > >> 1660 GO BP ids tested (9 have p< 0.01) > >> Selected gene set size: 427 > >> Gene universe size: 5616 > >> Annotation package: org.Sc.sgd > >> > >> when I used > >> > >> ps<-probeSetSummary(over,0.05) > >> > >> I got warning: > >> The vector of geneIds used to create the GOHyperGParamsobject > >> was not a > >> named vector. > >> If you want to know theprobesets that contributed to this result > >> either usea named vector for geneIds, or pass a vector of > >> probeset IDs > >> via sigProbesets. > >> when I use the input geneIDs (segene) to pass the vector via > >> sgProbesets > >> like: > >> > >> ps<-probeSetSummary(over,0.05,**,segene) //segene is input > >> yeast ORF ID > >> > >> I still got a empty resut. > >> Did I do something wrong? > >> > >> > >> Well if you actually used the code above, I am surprised it even > >> ran. Double commas usually result in an error. > >> > >> Also, please re-read the message you got from probeSetSummary(). > >> You are supposed to be passing in a vector of probeset IDs, not > >> re-sending the ORF IDs. > >> > >> Best, > >> > >> Jim > >> > >> > >> > >> Thanks for further help. > >> > >> Tim > >> > >> > >> > >> > >> > >> > >> > >> On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao@gmail.com> >> <mailto:yuan.x.hao@gmail.com>> wrote: > >> > >> > >> Would "probeSetSummary()" do what your want? > >> > >> Yuan > >> > >> > >> On 21 Jul 2012, at 02:47, Tim [guest] wrote: > >> > >> > >> Hi, > >> > >> I used GOstats to perform enrichment test on a set of > >> genes (20). > >> > >> There are 7 GO terms with pvalue less than cuttoff and > >> therefore shown in > >> the result table. > >> > >> How can I get the information that which gene in the > >> input gene set > >> belong to which GO term of these enriched GO terms? > >> > >> > >> > >> > >> best, > >> > >> Tim > >> > >> -- output of sessionInfo(): > >> Thanks for any comments. > >> > >> -- > >> Sent via the guest posting facility at > >> bioconductor.org <http: bioconductor.org="">. > >> > >> > >> ______________________________****_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> > >> > > >> > >> https://stat.ethz.ch/mailman/****listinfo/biocond uctor<https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor=""> > >> <https: **="" stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" s="" tat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >> > > >> Search the archives: http://news.gmane.org/gmane.** > >> science.biology.informatics.****conductor< > >> http://news.gmane.**org/gmane.science.biology.**informatics.condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >> > > >> > >> > >> [[alternative HTML version deleted]] > >> > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> > >> > > >> > >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<http s:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >> Search the archives: > >> http://news.gmane.org/gmane.**science.biology.informatics.** > >> conductor<http: news.gmane.org="" gmane.science.biology.informatics="" .conductor=""> > >> > >> > >> -- James W. MacDonald, M.S. > >> Biostatistician > >> University of Washington > >> Environmental and Occupational Health Sciences > >> 4225 Roosevelt Way NE, # 100 > >> Seattle WA 98105-6099 > >> > >> > >> > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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