Question: Genes annotated to GO:0031281 using org.Hs.eg.db
1
gravatar for Tim Smith
5.3 years ago by
Tim Smith1.1k
Tim Smith1.1k wrote:
Hi, I was trying to get the genes annotated to the GO term "GO:0031281". My code: library(org.Hs.eg.db) genes <- get("GO:0031281", org.Hs.egGO2EG) When I run the code, I get: > genes <- get("GO:0031281", org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :   value for "GO:0031281" not found If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? thanks! [[alternative HTML version deleted]]
go homo sapiens • 938 views
ADD COMMENTlink modified 5.3 years ago by James W. MacDonald50k • written 5.3 years ago by Tim Smith1.1k
Answer: Genes annotated to GO:0031281 using org.Hs.eg.db
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gravatar for James W. MacDonald
5.3 years ago by
United States
James W. MacDonald50k wrote:
Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS) IDA IDA TAS TAS IDA TAS IEA TAS TAS TAS "49" "116" "116" "117" "135" "135" "136" "136" "140" "153" IDA IDA TAS IDA IEA IDA IDA TAS IDA IEA "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" "1812" IDA IEA NAS TAS TAS IEA TAS TAS IEA TAS "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" "2778" IDA ISS ISS IBA IBA IMP ISS TAS TAS TAS "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" "5032" ISS NAS IEA IDA IEA TAS TAS "5578" "5894" "7077" "7432" "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL 1 GO:0031281 IDA BP 49 ACR 2 GO:0031281 IDA BP 116 ADCYAP1 3 GO:0031281 TAS BP 116 ADCYAP1 4 GO:0031281 TAS BP 117 ADCYAP1R1 5 GO:0031281 IDA BP 135 ADORA2A 6 GO:0031281 TAS BP 135 ADORA2A 7 GO:0031281 IEA BP 136 ADORA2B 8 GO:0031281 TAS BP 136 ADORA2B 9 GO:0031281 TAS BP 140 ADORA3 10 GO:0031281 TAS BP 153 ADRB1 11 GO:0031281 IDA BP 154 ADRB2 12 GO:0031281 IDA BP 155 ADRB3 13 GO:0031281 TAS BP 554 AVPR2 14 GO:0031281 IDA BP 796 CALCA 15 GO:0031281 IEA BP 796 CALCA 16 GO:0031281 IDA BP 799 CALCR 17 GO:0031281 IDA BP 1394 CRHR1 18 GO:0031281 TAS BP 1394 CRHR1 19 GO:0031281 IDA BP 1812 DRD1 20 GO:0031281 IEA BP 1812 DRD1 21 GO:0031281 IDA BP 1816 DRD5 22 GO:0031281 IEA BP 1816 DRD5 23 GO:0031281 NAS BP 1816 DRD5 24 GO:0031281 TAS BP 1816 DRD5 25 GO:0031281 TAS BP 1909 EDNRA 26 GO:0031281 IEA BP 2692 GHRHR 27 GO:0031281 TAS BP 2696 GIPR 28 GO:0031281 TAS BP 2740 GLP1R 29 GO:0031281 IEA BP 2774 GNAL 30 GO:0031281 TAS BP 2778 GNAS 31 GO:0031281 IDA BP 2852 GPER1 32 GO:0031281 ISS BP 3973 LHCGR 33 GO:0031281 ISS BP 4763 NF1 34 GO:0031281 IBA BP 4842 NOS1 35 GO:0031281 IBA BP 4843 NOS2 36 GO:0031281 IMP BP 4846 NOS3 37 GO:0031281 ISS BP 4846 NOS3 38 GO:0031281 TAS BP 4914 NTRK1 39 GO:0031281 TAS BP 4915 NTRK2 40 GO:0031281 TAS BP 5032 P2RY11 41 GO:0031281 ISS BP 5578 PRKCA 42 GO:0031281 NAS BP 5894 RAF1 43 GO:0031281 IEA BP 7077 TIMP2 44 GO:0031281 IDA BP 7432 VIP 45 GO:0031281 IEA BP 7434 VIPR2 46 GO:0031281 TAS BP 10486 CAP2 47 GO:0031281 TAS BP 10487 CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) : 'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x at ifnotfound) : > value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! > [[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
ADD COMMENTlink written 5.3 years ago by James W. MacDonald50k
Hi James, Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for which I was checking enrichment and I got this term as one of the significant terms. The details are:                GOBPID      Pvalue OddsRatio    ExpCount Count Size Term GO:0031281 0.021301601 10.113271  0.22913929     2   15 positive regulation of cyclase activity I used GOstats for this analysis. If Count = 2, then shouldn't there be two genes that are directly annotated to this term? On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS)     IDA    IDA    TAS    TAS    IDA    TAS    IEA    TAS TAS TAS     "49"  "116"  "116"  "117"  "135"  "135"  "136"  "136" "140" "153"     IDA    IDA    TAS    IDA    IEA    IDA    IDA    TAS IDA IEA   "154"  "155"  "554"  "796"  "796"  "799"  "1394"  "1394" "1812" "1812"     IDA    IEA    NAS    TAS    TAS    IEA    TAS    TAS IEA TAS   "1816"  "1816"  "1816"  "1816"  "1909"  "2692"  "2696"  "2740" "2774" "2778"     IDA    ISS    ISS    IBA    IBA    IMP    ISS    TAS TAS TAS   "2852"  "3973"  "4763"  "4842"  "4843"  "4846"  "4846"  "4914" "4915" "5032"     ISS    NAS    IEA    IDA    IEA    TAS    TAS   "5578"  "5894"  "7077"  "7432"  "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL")         GOALL EVIDENCEALL ONTOLOGYALL ENTREZID    SYMBOL 1  GO:0031281        IDA          BP      49      ACR 2  GO:0031281        IDA          BP      116  ADCYAP1 3  GO:0031281        TAS          BP      116  ADCYAP1 4  GO:0031281        TAS          BP      117 ADCYAP1R1 5  GO:0031281        IDA          BP      135  ADORA2A 6  GO:0031281        TAS          BP      135  ADORA2A 7  GO:0031281        IEA          BP      136  ADORA2B 8  GO:0031281        TAS          BP      136  ADORA2B 9  GO:0031281        TAS          BP      140    ADORA3 10 GO:0031281        TAS          BP      153    ADRB1 11 GO:0031281        IDA          BP      154    ADRB2 12 GO:0031281        IDA          BP      155    ADRB3 13 GO:0031281        TAS          BP      554    AVPR2 14 GO:0031281        IDA          BP      796    CALCA 15 GO:0031281        IEA          BP      796    CALCA 16 GO:0031281        IDA          BP      799    CALCR 17 GO:0031281        IDA          BP    1394    CRHR1 18 GO:0031281        TAS          BP    1394    CRHR1 19 GO:0031281        IDA          BP    1812      DRD1 20 GO:0031281        IEA          BP    1812      DRD1 21 GO:0031281        IDA          BP    1816      DRD5 22 GO:0031281        IEA          BP    1816      DRD5 23 GO:0031281        NAS          BP    1816      DRD5 24 GO:0031281        TAS          BP    1816      DRD5 25 GO:0031281        TAS          BP    1909    EDNRA 26 GO:0031281        IEA          BP    2692    GHRHR 27 GO:0031281        TAS          BP    2696      GIPR 28 GO:0031281        TAS          BP    2740    GLP1R 29 GO:0031281        IEA          BP    2774      GNAL 30 GO:0031281        TAS          BP    2778      GNAS 31 GO:0031281        IDA          BP    2852    GPER1 32 GO:0031281        ISS          BP    3973    LHCGR 33 GO:0031281        ISS          BP    4763      NF1 34 GO:0031281        IBA          BP    4842      NOS1 35 GO:0031281        IBA          BP    4843      NOS2 36 GO:0031281        IMP          BP    4846      NOS3 37 GO:0031281        ISS          BP    4846      NOS3 38 GO:0031281        TAS          BP    4914    NTRK1 39 GO:0031281        TAS          BP    4915    NTRK2 40 GO:0031281        TAS          BP    5032    P2RY11 41 GO:0031281        ISS          BP    5578    PRKCA 42 GO:0031281        NAS          BP    5894      RAF1 43 GO:0031281        IEA          BP    7077    TIMP2 44 GO:0031281        IDA          BP    7432      VIP 45 GO:0031281        IEA          BP    7434    VIPR2 46 GO:0031281        TAS          BP    10486      CAP2 47 GO:0031281        TAS          BP    10487      CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) :   'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : >    value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! >     [[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 -- 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]]
ADD REPLYlink written 5.3 years ago by Tim Smith1.1k
Hi James, Hmmm....I seem to get an error if I use probeSetSummary. As I mentioned before I run the hyperGTest using a set of genes (and not a set of probes). Here is what I get: hgOverGO <- hyperGTest(paramsGO) > hgOverGO Gene to GO BP Conditional test for over-representation 3843 GO BP ids tested (220 have p < 0.05) Selected gene set size: 318     Gene universe size: 6088     Annotation package: org.Hs.eg > class(hgOverGO) [1] "GOHyperGResult" attr(,"package") [1] "GOstats" > head(summary(hgOverGO))       GOBPID       Pvalue OddsRatio   ExpCount Count Size                                        Term 1 GO:0007268 2.658284e-07  2.645556 19.0653745    43  365                       synaptic transmission 2 GO:0001975 1.299252e-06 21.622722  0.6790407     7   13                     response to amphetamine 3 GO:0035637 2.726576e-06  2.320191 22.8784494    46  438          multicellular organismal signaling 4 GO:0072511 1.195032e-05  3.566708  6.2680683    19  120         divalent inorganic cation transport 5 GO:0018958 1.788607e-05  9.280645  1.2536137     8   24 phenol- containing compound metabolic process 6 GO:0042886 2.537415e-04  3.066360  5.9546649    16  114                             amide transport > ps <- probeSetSummary(hgOverGO,pvalue=0.05) Error in (function (classes, fdef, mtable)  :   unable to find an inherited method for function ‘columns’ for signature ‘"function"’ > traceback() 7: stop(gettextf("unable to find an inherited method for function %s for signature %s",        sQuote(fdef@generic), sQuote(cnames)), domain = NA) 6: (function (classes, fdef, mtable)    {        methods <- .findInheritedMethods(classes, fdef, mtable)        if (length(methods) == 1L)            return(methods[[1L]])        else if (length(methods) == 0L) {            cnames <- paste0("\"", sapply(classes, as.character),                "\"", collapse = ", ")            stop(gettextf("unable to find an inherited method for function %s for signature %s",                sQuote(fdef@generic), sQuote(cnames)), domain = NA)        }        else stop("Internal error in finding inherited methods; didn't return a unique method",            domain = NA)    })(list("function"), function (x)    standardGeneric("columns"), <environment>) 5: columns(db) 4: match(x, table, nomatch = 0L) 3: map %in% columns(db) 2: getAnnMap(ids, annotation(result)) 1: probeSetSummary(hgOverGO, pvalue = 0.05) Am I calling the probeSetSummary function incorrectly? thanks!! On Wednesday, March 19, 2014 5:54 PM, Tim Smith <tim_smith_666@yahoo.com> wrote: Hi James, Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for which I was checking enrichment and I got this term as one of the significant terms. The details are:                GOBPID      Pvalue OddsRatio    ExpCount Count Size                                                             Term GO:0031281 0.021301601 10.113271  0.22913929     2   15                          positive regulation of cyclase activity I used GOstats for this analysis. If Count = 2, then shouldn't there be two genes that are directly annotated to this term? On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, There may not be any IDs mapped to that term directly. You can use GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > get("GO:0031281", org.Hs.egGO2ALLEGS)      IDA     IDA     TAS     TAS     IDA     TAS     IEA     TAS TAS   TAS     "49"   "116"   "116"   "117"   "135"   "135"  "136"   "136" "140" "153"      IDA     IDA     TAS     IDA     IEA     IDA     IDA     TAS IDA   IEA    "154"   "155"   "554"   "796"   "796"   "799"  "1394" "1394" "1812" "1812"      IDA     IEA     NAS     TAS     TAS     IEA     TAS     TAS IEA   TAS   "1816"  "1816"  "1816"  "1816"  "1909"  "2692"  "2696" "2740" "2774" "2778"      IDA     ISS     ISS     IBA     IBA     IMP     ISS     TAS TAS   TAS   "2852"  "3973"  "4763"  "4842"  "4843"  "4846"  "4846" "4914" "4915" "5032"      ISS     NAS     IEA     IDA     IEA     TAS     TAS   "5578"  "5894"  "7077"  "7432"  "7434" "10486" "10487" Or the more powerful select() method: > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL")          GOALL EVIDENCEALL ONTOLOGYALL ENTREZID    SYMBOL 1  GO:0031281         IDA          BP       49      ACR 2  GO:0031281         IDA          BP      116  ADCYAP1 3  GO:0031281         TAS          BP      116  ADCYAP1 4  GO:0031281         TAS          BP      117 ADCYAP1R1 5  GO:0031281         IDA          BP      135  ADORA2A 6  GO:0031281         TAS          BP      135  ADORA2A 7  GO:0031281         IEA          BP      136  ADORA2B 8  GO:0031281         TAS          BP      136  ADORA2B 9  GO:0031281         TAS          BP      140   ADORA3 10 GO:0031281         TAS          BP      153    ADRB1 11 GO:0031281         IDA          BP      154    ADRB2 12 GO:0031281         IDA          BP      155    ADRB3 13 GO:0031281         TAS          BP      554    AVPR2 14 GO:0031281         IDA          BP      796    CALCA 15 GO:0031281         IEA          BP      796    CALCA 16 GO:0031281         IDA          BP      799    CALCR 17 GO:0031281         IDA          BP     1394    CRHR1 18 GO:0031281         TAS          BP     1394    CRHR1 19 GO:0031281         IDA          BP     1812     DRD1 20 GO:0031281         IEA          BP     1812     DRD1 21 GO:0031281         IDA          BP     1816     DRD5 22 GO:0031281         IEA          BP     1816     DRD5 23 GO:0031281         NAS          BP     1816     DRD5 24 GO:0031281         TAS          BP     1816     DRD5 25 GO:0031281         TAS          BP     1909    EDNRA 26 GO:0031281         IEA          BP     2692    GHRHR 27 GO:0031281         TAS          BP     2696     GIPR 28 GO:0031281         TAS          BP     2740    GLP1R 29 GO:0031281         IEA          BP     2774     GNAL 30 GO:0031281         TAS          BP     2778     GNAS 31 GO:0031281         IDA          BP     2852    GPER1 32 GO:0031281         ISS          BP     3973    LHCGR 33 GO:0031281         ISS          BP     4763      NF1 34 GO:0031281         IBA          BP     4842     NOS1 35 GO:0031281         IBA          BP     4843     NOS2 36 GO:0031281         IMP          BP     4846     NOS3 37 GO:0031281         ISS          BP     4846     NOS3 38 GO:0031281         TAS          BP     4914    NTRK1 39 GO:0031281         TAS          BP     4915    NTRK2 40 GO:0031281         TAS          BP     5032   P2RY11 41 GO:0031281         ISS          BP     5578    PRKCA 42 GO:0031281         NAS          BP     5894     RAF1 43 GO:0031281         IEA          BP     7077    TIMP2 44 GO:0031281         IDA          BP     7432      VIP 45 GO:0031281         IEA          BP     7434    VIPR2 46 GO:0031281         TAS          BP    10486     CAP2 47 GO:0031281         TAS          BP    10487     CAP1 Warning message: In .generateExtraRows(tab, keys, jointype) :    'select' resulted in 1:many mapping between keys and return rows Best, Jim On 3/19/2014 4:28 AM, Tim Smith wrote: > Hi, > > I was trying to get the genes annotated to the GO term "GO:0031281". My code: > > library(org.Hs.eg.db) > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > When I run the code, I get: > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : >    value for "GO:0031281" not found > > If I check in AMIGO for this GO term, it seems to have many gene products for Homo sapiens. Am I doing something wrong? Is there an alternate package that I can try, just to double check the results? > > thanks! >     [[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 -- 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]]
ADD REPLYlink written 5.3 years ago by Tim Smith1.1k
Hi Tim, Note that you _always_ use a set of genes for hyperGTest. Even if you started with an array, you can only count a significantly differentially expressed gene once. The difference here is that you used the org.Hs.eg.db package as the annotation rather than some array annotation package, so probeSetSummary() won't work, as it is trying to match things back to probe IDs. So you can do something like this: gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") gos <- summary(hgOverGO)[,1] golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) Best, Jim On 3/19/2014 7:03 PM, Tim Smith wrote: > Hi James, > > Hmmm....I seem to get an error if I use probeSetSummary. As I > mentioned before I run the hyperGTest using a set of genes (and not a > set of probes). > > Here is what I get: > > hgOverGO <- hyperGTest(paramsGO) > > > hgOverGO > Gene to GO BP Conditional test for over-representation > 3843 GO BP ids tested (220 have p < 0.05) > Selected gene set size: 318 > Gene universe size: 6088 > Annotation package: org.Hs.eg > > > class(hgOverGO) > [1] "GOHyperGResult" > attr(,"package") > [1] "GOstats" > > > head(summary(hgOverGO)) > GOBPID Pvalue OddsRatio ExpCount Count Size Term > 1 GO:0007268 2.658284e-07 2.645556 19.0653745 43 365 > synaptic transmission > 2 GO:0001975 1.299252e-06 21.622722 0.6790407 7 13 response > to amphetamine > 3 GO:0035637 2.726576e-06 2.320191 22.8784494 46 438 > multicellular organismal signaling > 4 GO:0072511 1.195032e-05 3.566708 6.2680683 19 120 > divalent inorganic cation transport > 5 GO:0018958 1.788607e-05 9.280645 1.2536137 8 24 > phenol-containing compound metabolic process > 6 GO:0042886 2.537415e-04 3.066360 5.9546649 16 114 > amide transport > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?columns? for > signature ?"function"? > > > traceback() > 7: stop(gettextf("unable to find an inherited method for function %s > for signature %s", > sQuote(fdef at generic), sQuote(cnames)), domain = NA) > 6: (function (classes, fdef, mtable) > { > methods <- .findInheritedMethods(classes, fdef, mtable) > if (length(methods) == 1L) > return(methods[[1L]]) > else if (length(methods) == 0L) { > cnames <- paste0("\"", sapply(classes, as.character), > "\"", collapse = ", ") > stop(gettextf("unable to find an inherited method for function %s for > signature %s", > sQuote(fdef at generic), sQuote(cnames)), domain = NA) > } > else stop("Internal error in finding inherited methods; didn't > return a unique method", > domain = NA) > })(list("function"), function (x) > standardGeneric("columns"), <environment>) > 5: columns(db) > 4: match(x, table, nomatch = 0L) > 3: map %in% columns(db) > 2: getAnnMap(ids, annotation(result)) > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > Am I calling the probeSetSummary function incorrectly? > > > thanks!! > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > <tim_smith_666 at="" yahoo.com=""> wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > > GOBPID Pvalue OddsRatio ExpCount Count Size > Term > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">> wrote: > > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > IDA IDA TAS TAS IDA TAS IEA TAS TAS > TAS > "49" "116" "116" "117" "135" "135" "136" "136" "140" > "153" > IDA IDA TAS IDA IEA IDA IDA TAS IDA > IEA > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > "1812" > IDA IEA NAS TAS TAS IEA TAS TAS IEA > TAS > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > "2778" > IDA ISS ISS IBA IBA IMP ISS TAS TAS > TAS > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > "5032" > ISS NAS IEA IDA IEA TAS TAS > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1 GO:0031281 IDA BP 49 ACR > 2 GO:0031281 IDA BP 116 ADCYAP1 > 3 GO:0031281 TAS BP 116 ADCYAP1 > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > 5 GO:0031281 IDA BP 135 ADORA2A > 6 GO:0031281 TAS BP 135 ADORA2A > 7 GO:0031281 IEA BP 136 ADORA2B > 8 GO:0031281 TAS BP 136 ADORA2B > 9 GO:0031281 TAS BP 140 ADORA3 > 10 GO:0031281 TAS BP 153 ADRB1 > 11 GO:0031281 IDA BP 154 ADRB2 > 12 GO:0031281 IDA BP 155 ADRB3 > 13 GO:0031281 TAS BP 554 AVPR2 > 14 GO:0031281 IDA BP 796 CALCA > 15 GO:0031281 IEA BP 796 CALCA > 16 GO:0031281 IDA BP 799 CALCR > 17 GO:0031281 IDA BP 1394 CRHR1 > 18 GO:0031281 TAS BP 1394 CRHR1 > 19 GO:0031281 IDA BP 1812 DRD1 > 20 GO:0031281 IEA BP 1812 DRD1 > 21 GO:0031281 IDA BP 1816 DRD5 > 22 GO:0031281 IEA BP 1816 DRD5 > 23 GO:0031281 NAS BP 1816 DRD5 > 24 GO:0031281 TAS BP 1816 DRD5 > 25 GO:0031281 TAS BP 1909 EDNRA > 26 GO:0031281 IEA BP 2692 GHRHR > 27 GO:0031281 TAS BP 2696 GIPR > 28 GO:0031281 TAS BP 2740 GLP1R > 29 GO:0031281 IEA BP 2774 GNAL > 30 GO:0031281 TAS BP 2778 GNAS > 31 GO:0031281 IDA BP 2852 GPER1 > 32 GO:0031281 ISS BP 3973 LHCGR > 33 GO:0031281 ISS BP 4763 NF1 > 34 GO:0031281 IBA BP 4842 NOS1 > 35 GO:0031281 IBA BP 4843 NOS2 > 36 GO:0031281 IMP BP 4846 NOS3 > 37 GO:0031281 ISS BP 4846 NOS3 > 38 GO:0031281 TAS BP 4914 NTRK1 > 39 GO:0031281 TAS BP 4915 NTRK2 > 40 GO:0031281 TAS BP 5032 P2RY11 > 41 GO:0031281 ISS BP 5578 PRKCA > 42 GO:0031281 NAS BP 5894 RAF1 > 43 GO:0031281 IEA BP 7077 TIMP2 > 44 GO:0031281 IDA BP 7432 VIP > 45 GO:0031281 IEA BP 7434 VIPR2 > 46 GO:0031281 TAS BP 10486 CAP2 > 47 GO:0031281 TAS BP 10487 CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : > 'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound="">) : > > value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > > [[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 > > [[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
ADD REPLYlink written 5.3 years ago by James W. MacDonald50k
1
Hi James, Thanks for that. However, the number of genes associated with the GO term with your code example, doesn't match the number of genes associated with that GO term with summary(hgOverGO): For example, my hgOverGO gives 43 genes annotated to the node: GOBPID Pvalue OddsRatio ExpCount Count Size Term GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 365 synaptic transmission While if I use your example code, it results in 53 genes. There are many such mismatches. Wouldn't it be great if GOstats gives the option of accessing the actual genes that it found annotated to a GO term? thanks !! On Thursday, March 20, 2014 10:38 AM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, Note that you _always_ use a set of genes for hyperGTest. Even if you started with an array, you can only count a significantly differentially expressed gene once. The difference here is that you used the org.Hs.eg.db package as the annotation rather than some array annotation package, so probeSetSummary() won't work, as it is trying to match things back to probe IDs. So you can do something like this: gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") gos <- summary(hgOverGO)[,1] golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) Best, Jim On 3/19/2014 7:03 PM, Tim Smith wrote: > Hi James, > > Hmmm....I seem to get an error if I use probeSetSummary. As I > mentioned before I run the hyperGTest using a set of genes (and not a > set of probes). > > Here is what I get: > > hgOverGO <- hyperGTest(paramsGO) > > > hgOverGO > Gene to GO BP Conditional test for over-representation > 3843 GO BP ids tested (220 have p < 0.05) > Selected gene set size: 318 >    Gene universe size: 6088 >    Annotation package: org.Hs.eg > > > class(hgOverGO) > [1] "GOHyperGResult" > attr(,"package") > [1] "GOstats" > > > head(summary(hgOverGO)) >      GOBPID Pvalue OddsRatio  ExpCount Count Size               Term > 1 GO:0007268 2.658284e-07  2.645556 19.0653745    43  365   >  synaptic transmission > 2 GO:0001975 1.299252e-06 21.622722  0.6790407    7  13   response > to amphetamine > 3 GO:0035637 2.726576e-06  2.320191 22.8784494    46  438 > multicellular organismal signaling > 4 GO:0072511 1.195032e-05  3.566708  6.2680683    19  120      >  divalent inorganic cation transport > 5 GO:0018958 1.788607e-05  9.280645  1.2536137    8  24 > phenol-containing compound metabolic process > 6 GO:0042886 2.537415e-04  3.066360  5.9546649    16  114        >  amide transport > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > Error in (function (classes, fdef, mtable)  : >  unable to find an inherited method for function ‘columns’ for > signature ‘"function"’ > > > traceback() > 7: stop(gettextf("unable to find an inherited method for function %s > for signature %s", >  sQuote(fdef@generic), sQuote(cnames)), domain = NA) > 6: (function (classes, fdef, mtable) >    { >        methods <- .findInheritedMethods(classes, fdef, mtable) >        if (length(methods) == 1L) >  return(methods[[1L]]) >        else if (length(methods) == 0L) { >            cnames <- paste0("\"", sapply(classes, as.character), >                "\"", collapse = ", ") >  stop(gettextf("unable to find an inherited method for function %s for > signature %s", >  sQuote(fdef@generic), sQuote(cnames)), domain = NA) >        } >        else stop("Internal error in finding inherited methods; didn't > return a unique method", >            domain = NA) >  })(list("function"), function (x) >  standardGeneric("columns"), <environment>) > 5: columns(db) > 4: match(x, table, nomatch = 0L) > 3: map %in% columns(db) > 2: getAnnMap(ids, annotation(result)) > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > Am I calling the probeSetSummary function incorrectly? > > > thanks!! > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > <tim_smith_666@yahoo.com> wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > >                GOBPID      Pvalue OddsRatio    ExpCount Count Size   >            Term > GO:0031281 0.021301601 10.113271  0.22913929    2  15            >            positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon@uw.edu <mailto:jmacdon@uw.edu="">> wrote: > > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) >      IDA    IDA    TAS    TAS    IDA    TAS IEA   TAS TAS > TAS >    "49"  "116"  "116"  "117"  "135"  "135" "136" "136" "140" > "153" >      IDA    IDA    TAS    IDA    IEA    IDA IDA   TAS IDA > IEA >    "154"  "155"  "554"  "796"  "796"  "799" "1394" "1394" "1812" > "1812" >      IDA    IEA    NAS    TAS    TAS    IEA TAS   TAS IEA > TAS >  "1816"  "1816"  "1816"  "1816"  "1909"  "2692" "2696" "2740" "2774" > "2778" >      IDA    ISS    ISS    IBA    IBA    IMP ISS   TAS TAS > TAS >  "2852"  "3973"  "4763"  "4842"  "4843"  "4846" "4846" "4914" "4915" > "5032" >      ISS    NAS    IEA    IDA    IEA    TAS   TAS >  "5578"  "5894"  "7077"  "7432"  "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") >          GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1  GO:0031281        IDA          BP      49     ACR > 2  GO:0031281        IDA          BP      116 ADCYAP1 > 3  GO:0031281        TAS          BP      116 ADCYAP1 > 4  GO:0031281        TAS          BP      117 ADCYAP1R1 > 5  GO:0031281        IDA          BP      135 ADORA2A > 6  GO:0031281        TAS          BP      135 ADORA2A > 7  GO:0031281        IEA          BP      136 ADORA2B > 8  GO:0031281        TAS          BP      136 ADORA2B > 9  GO:0031281        TAS          BP      140   ADORA3 > 10 GO:0031281        TAS          BP      153   ADRB1 > 11 GO:0031281        IDA          BP      154   ADRB2 > 12 GO:0031281        IDA          BP      155   ADRB3 > 13 GO:0031281        TAS          BP      554   AVPR2 > 14 GO:0031281        IDA          BP      796   CALCA > 15 GO:0031281        IEA          BP      796   CALCA > 16 GO:0031281        IDA          BP      799   CALCR > 17 GO:0031281        IDA          BP    1394   CRHR1 > 18 GO:0031281        TAS          BP    1394   CRHR1 > 19 GO:0031281        IDA          BP    1812     DRD1 > 20 GO:0031281        IEA          BP    1812     DRD1 > 21 GO:0031281        IDA          BP    1816     DRD5 > 22 GO:0031281        IEA          BP    1816     DRD5 > 23 GO:0031281        NAS          BP    1816     DRD5 > 24 GO:0031281        TAS          BP    1816     DRD5 > 25 GO:0031281        TAS          BP    1909   EDNRA > 26 GO:0031281        IEA          BP    2692   GHRHR > 27 GO:0031281        TAS          BP    2696     GIPR > 28 GO:0031281        TAS          BP    2740   GLP1R > 29 GO:0031281        IEA          BP    2774     GNAL > 30 GO:0031281        TAS          BP    2778     GNAS > 31 GO:0031281        IDA          BP    2852   GPER1 > 32 GO:0031281        ISS          BP    3973   LHCGR > 33 GO:0031281        ISS          BP    4763     NF1 > 34 GO:0031281        IBA          BP    4842     NOS1 > 35 GO:0031281        IBA          BP    4843     NOS2 > 36 GO:0031281        IMP          BP    4846     NOS3 > 37 GO:0031281        ISS          BP    4846     NOS3 > 38 GO:0031281        TAS          BP    4914   NTRK1 > 39 GO:0031281        TAS          BP    4915   NTRK2 > 40 GO:0031281        TAS          BP    5032   P2RY11 > 41 GO:0031281        ISS          BP    5578   PRKCA > 42 GO:0031281        NAS          BP    5894     RAF1 > 43 GO:0031281        IEA          BP    7077   TIMP2 > 44 GO:0031281        IDA          BP    7432     VIP > 45 GO:0031281        IEA          BP    7434   VIPR2 > 46 GO:0031281        TAS          BP    10486     CAP2 > 47 GO:0031281        TAS          BP    10487     CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : >    'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x@ifnotfound > <mailto:x@ifnotfound>) : > >    value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > >    [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@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 > >    [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.3 years ago by Tim Smith1.1k
Hi Tim, Different approach. gos <- summary(hgOverGO)[,1] gIU <- geneIdUniverse(hgOverGO)[gos] gns <- geneIds(hgOverGO) golst <- lapply(gIU, function(x) x[x %in% gns]) And as a test > univ <- keys(org.Hs.eg.db) > set.seed(0xabeef) > gns <- sample(300, univ) > p <- new(:GOHyperGParams, geneIds = gns, universeGeneIds = univ, ontology = "BP", annotation = "org.Hs.eg.db") > hyp <- hyperGTest(p) > gos <- summary(hyp)[,1] > gIU <- geneIdUniverse(hyp)[gos] > golst <- lapply(gIU, function(x) x[x %in% gns]) > all.equal(summary(hyp)[,"Count"], sapply(golst, length), check.attributes = FALSE) [1] TRUE Best, Jim On 3/21/2014 8:12 PM, Tim Smith wrote: > Hi James, > > Thanks for that. However, the number of genes associated with the GO > term with your code example, doesn't match the number of genes > associated with that GO term with summary(hgOverGO): > > For example, my hgOverGO gives 43 genes annotated to the node: > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 > 365 synaptic transmission > > While if I use your example code, it results in 53 genes. There are > many such mismatches. Wouldn't it be great if GOstats gives the option > of accessing the actual genes that it found annotated to a GO term? > > thanks !! > > > > > > > On Thursday, March 20, 2014 10:38 AM, James W. MacDonald > <jmacdon at="" uw.edu=""> wrote: > Hi Tim, > > Note that you _always_ use a set of genes for hyperGTest. Even if you > started with an array, you can only count a significantly differentially > expressed gene once. > > The difference here is that you used the org.Hs.eg.db package as the > annotation rather than some array annotation package, so > probeSetSummary() won't work, as it is trying to match things back to > probe IDs. > > So you can do something like this: > > gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") > gos <- summary(hgOverGO)[,1] > golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) > > Best, > > Jim > > > > On 3/19/2014 7:03 PM, Tim Smith wrote: > > Hi James, > > > > Hmmm....I seem to get an error if I use probeSetSummary. As I > > mentioned before I run the hyperGTest using a set of genes (and not a > > set of probes). > > > > Here is what I get: > > > > hgOverGO <- hyperGTest(paramsGO) > > > > > hgOverGO > > Gene to GO BP Conditional test for over-representation > > 3843 GO BP ids tested (220 have p < 0.05) > > Selected gene set size: 318 > > Gene universe size: 6088 > > Annotation package: org.Hs.eg > > > > > class(hgOverGO) > > [1] "GOHyperGResult" > > attr(,"package") > > [1] "GOstats" > > > > > head(summary(hgOverGO)) > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > > 1 GO:0007268 2.658284e-07 2.645556 19.0653745 43 365 > > synaptic transmission > > 2 GO:0001975 1.299252e-06 21.622722 0.6790407 7 13 response > > to amphetamine > > 3 GO:0035637 2.726576e-06 2.320191 22.8784494 46 438 > > multicellular organismal signaling > > 4 GO:0072511 1.195032e-05 3.566708 6.2680683 19 120 > > divalent inorganic cation transport > > 5 GO:0018958 1.788607e-05 9.280645 1.2536137 8 24 > > phenol-containing compound metabolic process > > 6 GO:0042886 2.537415e-04 3.066360 5.9546649 16 114 > > amide transport > > > > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > > Error in (function (classes, fdef, mtable) : > > unable to find an inherited method for function ?columns? for > > signature ?"function"? > > > > > traceback() > > 7: stop(gettextf("unable to find an inherited method for function %s > > for signature %s", > > sQuote(fdef at generic <mailto:fdef at="" generic="">), sQuote(cnames)), domain > = NA) > > 6: (function (classes, fdef, mtable) > > { > > methods <- .findInheritedMethods(classes, fdef, mtable) > > if (length(methods) == 1L) > > return(methods[[1L]]) > > else if (length(methods) == 0L) { > > cnames <- paste0("\"", sapply(classes, as.character), > > "\"", collapse = ", ") > > stop(gettextf("unable to find an inherited method for function %s for > > signature %s", > > sQuote(fdef at generic <mailto:fdef at="" generic="">), sQuote(cnames)), domain > = NA) > > } > > else stop("Internal error in finding inherited methods; didn't > > return a unique method", > > domain = NA) > > })(list("function"), function (x) > > standardGeneric("columns"), <environment>) > > 5: columns(db) > > 4: match(x, table, nomatch = 0L) > > 3: map %in% columns(db) > > 2: getAnnMap(ids, annotation(result)) > > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > > > > Am I calling the probeSetSummary function incorrectly? > > > > > > thanks!! > > > > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > > <tim_smith_666 at="" yahoo.com="" <mailto:tim_smith_666="" at="" yahoo.com="">> wrote: > > Hi James, > > > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > > which I was checking enrichment and I got this term as one of the > > significant terms. The details are: > > > > GOBPID Pvalue OddsRatio ExpCount Count Size > > Term > > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > > positive regulation of cyclase activity > > > > I used GOstats for this analysis. If Count = 2, then shouldn't there > > be two genes that are directly annotated to this term? > > > > > > > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > > > Hi Tim, > > > > There may not be any IDs mapped to that term directly. You can use > > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > > IDA IDA TAS TAS IDA TAS IEA TAS TAS > > TAS > > "49" "116" "116" "117" "135" "135" "136" "136" "140" > > "153" > > IDA IDA TAS IDA IEA IDA IDA TAS IDA > > IEA > > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > > "1812" > > IDA IEA NAS TAS TAS IEA TAS TAS IEA > > TAS > > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > > "2778" > > IDA ISS ISS IBA IBA IMP ISS TAS TAS > > TAS > > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > > "5032" > > ISS NAS IEA IDA IEA TAS TAS > > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > > > Or the more powerful select() method: > > > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > > 1 GO:0031281 IDA BP 49 ACR > > 2 GO:0031281 IDA BP 116 ADCYAP1 > > 3 GO:0031281 TAS BP 116 ADCYAP1 > > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > > 5 GO:0031281 IDA BP 135 ADORA2A > > 6 GO:0031281 TAS BP 135 ADORA2A > > 7 GO:0031281 IEA BP 136 ADORA2B > > 8 GO:0031281 TAS BP 136 ADORA2B > > 9 GO:0031281 TAS BP 140 ADORA3 > > 10 GO:0031281 TAS BP 153 ADRB1 > > 11 GO:0031281 IDA BP 154 ADRB2 > > 12 GO:0031281 IDA BP 155 ADRB3 > > 13 GO:0031281 TAS BP 554 AVPR2 > > 14 GO:0031281 IDA BP 796 CALCA > > 15 GO:0031281 IEA BP 796 CALCA > > 16 GO:0031281 IDA BP 799 CALCR > > 17 GO:0031281 IDA BP 1394 CRHR1 > > 18 GO:0031281 TAS BP 1394 CRHR1 > > 19 GO:0031281 IDA BP 1812 DRD1 > > 20 GO:0031281 IEA BP 1812 DRD1 > > 21 GO:0031281 IDA BP 1816 DRD5 > > 22 GO:0031281 IEA BP 1816 DRD5 > > 23 GO:0031281 NAS BP 1816 DRD5 > > 24 GO:0031281 TAS BP 1816 DRD5 > > 25 GO:0031281 TAS BP 1909 EDNRA > > 26 GO:0031281 IEA BP 2692 GHRHR > > 27 GO:0031281 TAS BP 2696 GIPR > > 28 GO:0031281 TAS BP 2740 GLP1R > > 29 GO:0031281 IEA BP 2774 GNAL > > 30 GO:0031281 TAS BP 2778 GNAS > > 31 GO:0031281 IDA BP 2852 GPER1 > > 32 GO:0031281 ISS BP 3973 LHCGR > > 33 GO:0031281 ISS BP 4763 NF1 > > 34 GO:0031281 IBA BP 4842 NOS1 > > 35 GO:0031281 IBA BP 4843 NOS2 > > 36 GO:0031281 IMP BP 4846 NOS3 > > 37 GO:0031281 ISS BP 4846 NOS3 > > 38 GO:0031281 TAS BP 4914 NTRK1 > > 39 GO:0031281 TAS BP 4915 NTRK2 > > 40 GO:0031281 TAS BP 5032 P2RY11 > > 41 GO:0031281 ISS BP 5578 PRKCA > > 42 GO:0031281 NAS BP 5894 RAF1 > > 43 GO:0031281 IEA BP 7077 TIMP2 > > 44 GO:0031281 IDA BP 7432 VIP > > 45 GO:0031281 IEA BP 7434 VIPR2 > > 46 GO:0031281 TAS BP 10486 CAP2 > > 47 GO:0031281 TAS BP 10487 CAP1 > > Warning message: > > In .generateExtraRows(tab, keys, jointype) : > > 'select' resulted in 1:many mapping between keys and return rows > > > > Best, > > > > Jim > > > > > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > > Hi, > > > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > > My code: > > > > > > library(org.Hs.eg.db) > > > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > > > When I run the code, I get: > > > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound=""> > > <mailto:x at="" ifnotfound="" <mailto:x="" at="" ifnotfound="">>) : > > > value for "GO:0031281" not found > > > > > > If I check in AMIGO for this GO term, it seems to have many gene > > products for Homo sapiens. Am I doing something wrong? Is there an > > alternate package that I can try, just to double check the results? > > > > > > thanks! > > > [[alternative HTML version deleted]] > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto: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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto: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
ADD REPLYlink written 5.3 years ago by James W. MacDonald50k
Thanks Jim -  I think you've cracked it!! On Monday, March 24, 2014 12:01 PM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Tim, Different approach. gos <- summary(hgOverGO)[,1] gIU <- geneIdUniverse(hgOverGO)[gos] gns <- geneIds(hgOverGO) golst <- lapply(gIU, function(x) x[x %in% gns]) And as a test > univ <- keys(org.Hs.eg.db) > set.seed(0xabeef) > gns <- sample(300, univ) > p <- new(:GOHyperGParams, geneIds = gns, universeGeneIds = univ, ontology = "BP", annotation = "org.Hs.eg.db") > hyp <- hyperGTest(p) > gos <- summary(hyp)[,1] > gIU <- geneIdUniverse(hyp)[gos] > golst <- lapply(gIU, function(x) x[x %in% gns]) > all.equal(summary(hyp)[,"Count"], sapply(golst, length), check.attributes = FALSE) [1] TRUE Best, Jim On 3/21/2014 8:12 PM, Tim Smith wrote: > Hi James, > > Thanks for that. However, the number of genes associated with the GO > term with your code example, doesn't match the number of genes > associated with that GO term with summary(hgOverGO): > > For example, my hgOverGO gives 43 genes annotated to the node: > > GOBPID Pvalue OddsRatio ExpCount Count Size Term > GO:0007268 2.65828422773352e-07 2.64555618294749 19.0653745072273 43 > 365 synaptic transmission > > While if I use your example code, it results in 53 genes. There are > many such mismatches. Wouldn't it be great if GOstats gives the option > of accessing the actual genes that it found annotated to a GO term? > > thanks !! > > > > > > > On Thursday, March 20, 2014 10:38 AM, James W. MacDonald > <jmacdon@uw.edu> wrote: > Hi Tim, > > Note that you _always_ use a set of genes for hyperGTest. Even if you > started with an array, you can only count a significantly differentially > expressed gene once. > > The difference here is that you used the org.Hs.eg.db package as the > annotation rather than some array annotation package, so > probeSetSummary() won't work, as it is trying to match things back to > probe IDs. > > So you can do something like this: > > gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL") > gos <- summary(hgOverGO)[,1] > golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,]) > > Best, > > Jim > > > > On 3/19/2014 7:03 PM, Tim Smith wrote: > > Hi James, > > > > Hmmm....I seem to get an error if I use probeSetSummary. As I > > mentioned before I run the hyperGTest using a set of genes (and not a > > set of probes). > > > > Here is what I get: > > > > hgOverGO <- hyperGTest(paramsGO) > > > > > hgOverGO > > Gene to GO BP Conditional test for over-representation > > 3843 GO BP ids tested (220 have p < 0.05) > > Selected gene set size: 318 > >    Gene universe size: 6088 > >    Annotation package: org.Hs.eg > > > > > class(hgOverGO) > > [1] "GOHyperGResult" > > attr(,"package") > > [1] "GOstats" > > > > > head(summary(hgOverGO)) > >      GOBPID Pvalue OddsRatio  ExpCount Count Size             Term > > 1 GO:0007268 2.658284e-07  2.645556 19.0653745 43  365 > >  synaptic transmission > > 2 GO:0001975 1.299252e-06 21.622722  0.6790407 7  13   response > > to amphetamine > > 3 GO:0035637 2.726576e-06  2.320191 22.8784494 46  438 > > multicellular organismal signaling > > 4 GO:0072511 1.195032e-05  3.566708  6.2680683 19  120 > >  divalent inorganic cation transport > > 5 GO:0018958 1.788607e-05  9.280645  1.2536137 8  24 > > phenol-containing compound metabolic process > > 6 GO:0042886 2.537415e-04  3.066360  5.9546649 16  114 > >  amide transport > > > > > > > ps <- probeSetSummary(hgOverGO,pvalue=0.05) > > Error in (function (classes, fdef, mtable)  : > >  unable to find an inherited method for function ‘columns’ for > > signature ‘"function"’ > > > > > traceback() > > 7: stop(gettextf("unable to find an inherited method for function %s > > for signature %s", > >  sQuote(fdef@generic <mailto:fdef@generic>), sQuote(cnames)), domain > = NA) > > 6: (function (classes, fdef, mtable) > >    { > >        methods <- .findInheritedMethods(classes, fdef, mtable) > >        if (length(methods) == 1L) > >  return(methods[[1L]]) > >        else if (length(methods) == 0L) { > >            cnames <- paste0("\"", sapply(classes, as.character), > >                "\"", collapse = ", ") > >  stop(gettextf("unable to find an inherited method for function %s for > > signature %s", > >  sQuote(fdef@generic <mailto:fdef@generic>), sQuote(cnames)), domain > = NA) > >        } > >        else stop("Internal error in finding inherited methods; didn't > > return a unique method", > >            domain = NA) > >  })(list("function"), function (x) > >  standardGeneric("columns"), <environment>) > > 5: columns(db) > > 4: match(x, table, nomatch = 0L) > > 3: map %in% columns(db) > > 2: getAnnMap(ids, annotation(result)) > > 1: probeSetSummary(hgOverGO, pvalue = 0.05) > > > > > > Am I calling the probeSetSummary function incorrectly? > > > > > > thanks!! > > > > > > On Wednesday, March 19, 2014 5:54 PM, Tim Smith > > <tim_smith_666@yahoo.com <mailto:tim_smith_666@yahoo.com="">> wrote: > > Hi James, > > > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > > which I was checking enrichment and I got this term as one of the > > significant terms. The details are: > > > >                GOBPID      Pvalue OddsRatio ExpCount Count Size > >            Term > > GO:0031281 0.021301601 10.113271  0.22913929    2 15 > >            positive regulation of cyclase activity > > > > I used GOstats for this analysis. If Count = 2, then shouldn't there > > be two genes that are directly annotated to this term? > > > > > > > > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > > <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu>>> wrote: > > > > Hi Tim, > > > > There may not be any IDs mapped to that term directly. You can use > > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > >      IDA    IDA    TAS    TAS    IDA    TAS IEA TAS TAS > > TAS > >    "49"  "116"  "116"  "117"  "135"  "135" "136" "136" "140" > > "153" > >      IDA    IDA    TAS    IDA    IEA    IDA IDA TAS IDA > > IEA > >    "154"  "155"  "554"  "796"  "796"  "799" "1394" "1394" "1812" > > "1812" > >      IDA    IEA    NAS    TAS    TAS    IEA TAS TAS IEA > > TAS > >  "1816"  "1816"  "1816"  "1816"  "1909"  "2692" "2696" "2740" "2774" > > "2778" > >      IDA    ISS    ISS    IBA    IBA    IMP ISS TAS TAS > > TAS > >  "2852"  "3973"  "4763"  "4842"  "4843"  "4846" "4846" "4914" "4915" > > "5032" > >      ISS    NAS    IEA    IDA    IEA    TAS    TAS > >  "5578"  "5894"  "7077"  "7432"  "7434" "10486" "10487" > > > > Or the more powerful select() method: > > > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > >          GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > > 1  GO:0031281        IDA          BP      49 ACR > > 2  GO:0031281        IDA          BP      116 ADCYAP1 > > 3  GO:0031281        TAS          BP      116 ADCYAP1 > > 4  GO:0031281        TAS          BP      117 ADCYAP1R1 > > 5  GO:0031281        IDA          BP      135 ADORA2A > > 6  GO:0031281        TAS          BP      135 ADORA2A > > 7  GO:0031281        IEA          BP      136 ADORA2B > > 8  GO:0031281        TAS          BP      136 ADORA2B > > 9  GO:0031281        TAS          BP      140 ADORA3 > > 10 GO:0031281        TAS          BP      153 ADRB1 > > 11 GO:0031281        IDA          BP      154 ADRB2 > > 12 GO:0031281        IDA          BP      155 ADRB3 > > 13 GO:0031281        TAS          BP      554 AVPR2 > > 14 GO:0031281        IDA          BP      796 CALCA > > 15 GO:0031281        IEA          BP      796 CALCA > > 16 GO:0031281        IDA          BP      799 CALCR > > 17 GO:0031281        IDA          BP    1394 CRHR1 > > 18 GO:0031281        TAS          BP    1394 CRHR1 > > 19 GO:0031281        IDA          BP    1812 DRD1 > > 20 GO:0031281        IEA          BP    1812 DRD1 > > 21 GO:0031281        IDA          BP    1816 DRD5 > > 22 GO:0031281        IEA          BP    1816 DRD5 > > 23 GO:0031281        NAS          BP    1816 DRD5 > > 24 GO:0031281        TAS          BP    1816 DRD5 > > 25 GO:0031281        TAS          BP    1909 EDNRA > > 26 GO:0031281        IEA          BP    2692 GHRHR > > 27 GO:0031281        TAS          BP    2696 GIPR > > 28 GO:0031281        TAS          BP    2740 GLP1R > > 29 GO:0031281        IEA          BP    2774 GNAL > > 30 GO:0031281        TAS          BP    2778 GNAS > > 31 GO:0031281        IDA          BP    2852 GPER1 > > 32 GO:0031281        ISS          BP    3973 LHCGR > > 33 GO:0031281        ISS          BP    4763 NF1 > > 34 GO:0031281        IBA          BP    4842 NOS1 > > 35 GO:0031281        IBA          BP    4843 NOS2 > > 36 GO:0031281        IMP          BP    4846 NOS3 > > 37 GO:0031281        ISS          BP    4846 NOS3 > > 38 GO:0031281        TAS          BP    4914 NTRK1 > > 39 GO:0031281        TAS          BP    4915 NTRK2 > > 40 GO:0031281        TAS          BP    5032 P2RY11 > > 41 GO:0031281        ISS          BP    5578 PRKCA > > 42 GO:0031281        NAS          BP    5894 RAF1 > > 43 GO:0031281        IEA          BP    7077 TIMP2 > > 44 GO:0031281        IDA          BP    7432 VIP > > 45 GO:0031281        IEA          BP    7434 VIPR2 > > 46 GO:0031281        TAS          BP    10486 CAP2 > > 47 GO:0031281        TAS          BP    10487 CAP1 > > Warning message: > > In .generateExtraRows(tab, keys, jointype) : > >    'select' resulted in 1:many mapping between keys and return rows > > > > Best, > > > > Jim > > > > > > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > > Hi, > > > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > > My code: > > > > > > library(org.Hs.eg.db) > > > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > > > When I run the code, I get: > > > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > > Error in .checkKeys(value, Rkeys(x), x@ifnotfound > <mailto:x@ifnotfound> > > <mailto:x@ifnotfound <mailto:x@ifnotfound="">>) : > > >    value for "GO:0031281" not found > > > > > > If I check in AMIGO for this GO term, it seems to have many gene > > products for Homo sapiens. Am I doing something wrong? Is there an > > alternate package that I can try, just to double check the results? > > > > > > thanks! > > >    [[alternative HTML version deleted]] > > > > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org <mailto:bioconductor@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 > > > >    [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org <mailto:bioconductor@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 [[alternative HTML version deleted]]
ADD REPLYlink written 5.3 years ago by Tim Smith1.1k
Hi Tim, See ?probeSetSummary. As an example, after running the example for that function, you end up with a GOHyperGResults object called 'hyp': > head(summary(hyp)) GOBPID Pvalue OddsRatio ExpCount Count Size 1 GO:0031399 5.316815e-15 3.623932 28.94921 72 397 2 GO:0036211 2.482766e-14 2.949456 56.00249 107 768 3 GO:0023052 1.756878e-13 2.816284 110.47367 164 1515 And the first GO term has 72 significant genes out of 397 available. The 'ps' object is a list created by the probeSetSummary function, and each list item presents the Entrez Gene ID, Probeset ID, and an indicator showing it the probeset gave rise to the significant result (not really necessary - you could just use unique() on the EntrezID column if you wanted to): > head(ps[["GO:0031399"]]) EntrezID ProbeSetID selected 1 10114 102_at 1 2 10114 41501_at 0 3 10114 41502_at 0 4 10188 1134_at 1 And > sum(ps[["GO:0031399"]]$selected) [1] 72 Note that you either have to use a _named_ vector of geneIds when you set up your GOHyperGParams object > head(prbs) 1000_at 1001_at 1002_f_at 1003_s_at 1005_at 1006_at "5595" "7075" "1557" "643" "1843" "4319" as is done in that example, or you can pass in a set of IDs using the 'sigProbesets' argument to probeSetSummary(). Or you can just subset to the unique Entrez Gene IDs in whichever list item you are interested in. Best, Jim On 3/19/2014 5:17 PM, Tim Smith wrote: > Hi James, > > Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for > which I was checking enrichment and I got this term as one of the > significant terms. The details are: > > GOBPID Pvalue OddsRatio ExpCount Count Size > Term > GO:0031281 0.021301601 10.113271 0.22913929 2 15 > positive regulation of cyclase activity > > I used GOstats for this analysis. If Count = 2, then shouldn't there > be two genes that are directly annotated to this term? > > > > > On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald > <jmacdon at="" uw.edu=""> wrote: > Hi Tim, > > There may not be any IDs mapped to that term directly. You can use > GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs. > > > get("GO:0031281", org.Hs.egGO2ALLEGS) > IDA IDA TAS TAS IDA TAS IEA TAS TAS > TAS > "49" "116" "116" "117" "135" "135" "136" "136" "140" > "153" > IDA IDA TAS IDA IEA IDA IDA TAS IDA > IEA > "154" "155" "554" "796" "796" "799" "1394" "1394" "1812" > "1812" > IDA IEA NAS TAS TAS IEA TAS TAS IEA > TAS > "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774" > "2778" > IDA ISS ISS IBA IBA IMP ISS TAS TAS > TAS > "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915" > "5032" > ISS NAS IEA IDA IEA TAS TAS > "5578" "5894" "7077" "7432" "7434" "10486" "10487" > > Or the more powerful select() method: > > > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL") > GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL > 1 GO:0031281 IDA BP 49 ACR > 2 GO:0031281 IDA BP 116 ADCYAP1 > 3 GO:0031281 TAS BP 116 ADCYAP1 > 4 GO:0031281 TAS BP 117 ADCYAP1R1 > 5 GO:0031281 IDA BP 135 ADORA2A > 6 GO:0031281 TAS BP 135 ADORA2A > 7 GO:0031281 IEA BP 136 ADORA2B > 8 GO:0031281 TAS BP 136 ADORA2B > 9 GO:0031281 TAS BP 140 ADORA3 > 10 GO:0031281 TAS BP 153 ADRB1 > 11 GO:0031281 IDA BP 154 ADRB2 > 12 GO:0031281 IDA BP 155 ADRB3 > 13 GO:0031281 TAS BP 554 AVPR2 > 14 GO:0031281 IDA BP 796 CALCA > 15 GO:0031281 IEA BP 796 CALCA > 16 GO:0031281 IDA BP 799 CALCR > 17 GO:0031281 IDA BP 1394 CRHR1 > 18 GO:0031281 TAS BP 1394 CRHR1 > 19 GO:0031281 IDA BP 1812 DRD1 > 20 GO:0031281 IEA BP 1812 DRD1 > 21 GO:0031281 IDA BP 1816 DRD5 > 22 GO:0031281 IEA BP 1816 DRD5 > 23 GO:0031281 NAS BP 1816 DRD5 > 24 GO:0031281 TAS BP 1816 DRD5 > 25 GO:0031281 TAS BP 1909 EDNRA > 26 GO:0031281 IEA BP 2692 GHRHR > 27 GO:0031281 TAS BP 2696 GIPR > 28 GO:0031281 TAS BP 2740 GLP1R > 29 GO:0031281 IEA BP 2774 GNAL > 30 GO:0031281 TAS BP 2778 GNAS > 31 GO:0031281 IDA BP 2852 GPER1 > 32 GO:0031281 ISS BP 3973 LHCGR > 33 GO:0031281 ISS BP 4763 NF1 > 34 GO:0031281 IBA BP 4842 NOS1 > 35 GO:0031281 IBA BP 4843 NOS2 > 36 GO:0031281 IMP BP 4846 NOS3 > 37 GO:0031281 ISS BP 4846 NOS3 > 38 GO:0031281 TAS BP 4914 NTRK1 > 39 GO:0031281 TAS BP 4915 NTRK2 > 40 GO:0031281 TAS BP 5032 P2RY11 > 41 GO:0031281 ISS BP 5578 PRKCA > 42 GO:0031281 NAS BP 5894 RAF1 > 43 GO:0031281 IEA BP 7077 TIMP2 > 44 GO:0031281 IDA BP 7432 VIP > 45 GO:0031281 IEA BP 7434 VIPR2 > 46 GO:0031281 TAS BP 10486 CAP2 > 47 GO:0031281 TAS BP 10487 CAP1 > Warning message: > In .generateExtraRows(tab, keys, jointype) : > 'select' resulted in 1:many mapping between keys and return rows > > Best, > > Jim > > > On 3/19/2014 4:28 AM, Tim Smith wrote: > > Hi, > > > > I was trying to get the genes annotated to the GO term "GO:0031281". > My code: > > > > library(org.Hs.eg.db) > > > > genes <- get("GO:0031281", org.Hs.egGO2EG) > > > > When I run the code, I get: > > > >> genes <- get("GO:0031281", org.Hs.egGO2EG) > > Error in .checkKeys(value, Rkeys(x), x at ifnotfound > <mailto:x at="" ifnotfound="">) : > > value for "GO:0031281" not found > > > > If I check in AMIGO for this GO term, it seems to have many gene > products for Homo sapiens. Am I doing something wrong? Is there an > alternate package that I can try, just to double check the results? > > > > thanks! > > [[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
ADD REPLYlink written 5.3 years ago by James W. MacDonald50k
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