Question: serious problem with GOstats package
0
gravatar for gregory voisin
5.9 years ago by
Canada
gregory voisin430 wrote:
Hi, FOr my current analysis, I use GOstats package because it's a good, basic, simple package. I don't know why but since some time , when I use this code: params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = universeGeneIds , ontology=onto, pvalueCutoff= 0.01,conditional=FALSE,testDirection="over")  hgOver <- hyperGTest(params) I have this error message: Erreur dans eapply(ID2GO(datPkg), function(goids) { :   erreur d'évaluation de l'argument 'env' lors de la sélection d'une méthode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable)  :   unable to find an inherited method for function ‘cols’ for signature ‘"function"’ I have tested with R2.15.1, 2.12.! always the same problem. I think that the update of the package is sometimes problematic. If you have a solution, a suggestion or an alternative ( I'm going to see topGO)  Thanks for your help > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_Canada.1252  LC_CTYPE=French_Canada.1252    LC_MONETARY=French_Canada.1252 [4] LC_NUMERIC=C                   LC_TIME=French_Canada.1252    attached base packages: [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     other attached packages:  [1] hgu95av2.db_2.9.0    org.Hs.eg.db_2.9.0   ALL_1.4.14          topGO_2.12.0         [5] SparseM_0.99         GO.db_2.9.0          GOstats_2.26.0       RSQLite_0.11.3       [9] DBI_0.2-6            graph_1.38.0        Category_2.26.0      AnnotationDbi_1.22.5 [13] Biobase_2.20.0       BiocGenerics_0.6.0   limma_3.16.3        BiocInstaller_1.10.1 loaded via a namespace (and not attached):  [1] annotate_1.38.0       AnnotationForge_1.2.1 genefilter_1.42.0     grid_3.0.0            [5] GSEABase_1.22.0       IRanges_1.18.0        lattice_0.20-15       RBGL_1.36.2           [9] splines_3.0.0         stats4_3.0.0          survival_2.37-4       tools_3.0.0          [13] XML_3.96-1.1          xtable_1.7-1         > [[alternative HTML version deleted]]
go hgu95av2 gostats • 665 views
ADD COMMENTlink modified 5.9 years ago by Dan Tenenbaum8.2k • written 5.9 years ago by gregory voisin430
Answer: serious problem with GOstats package
0
gravatar for Dan Tenenbaum
5.9 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Gregory, On Wed, May 8, 2013 at 8:38 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: > Hi, > > FOr my current analysis, I use GOstats package because it's a good, basic, simple package. > I don't know why but since some time , > > when I use this code: > > params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = universeGeneIds , ontology=onto, pvalueCutoff= 0.01,conditional=FALSE,testDirection="over") What are the values of sigLL, universeGeneIds, and onto? Please post a complete reproducible example. Thanks, Dan > > hgOver <- hyperGTest(params) > > I have this error message: > > > Erreur dans eapply(ID2GO(datPkg), function(goids) { : > erreur d'?valuation de l'argument 'env' lors de la s?lection d'une m?thode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable) : > unable to find an inherited method for function ?cols? for signature ?"function"? > > I have tested with R2.15.1, 2.12.! always the same problem. I think that the update of the package is sometimes problematic. > > > If you have a solution, a suggestion or an alternative ( I'm going to see topGO) > > > > Thanks for your help > > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252 LC_MONETARY=French_Canada.1252 > [4] LC_NUMERIC=C LC_TIME=French_Canada.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.9.0 org.Hs.eg.db_2.9.0 ALL_1.4.14 topGO_2.12.0 > [5] SparseM_0.99 GO.db_2.9.0 GOstats_2.26.0 RSQLite_0.11.3 > [9] DBI_0.2-6 graph_1.38.0 Category_2.26.0 AnnotationDbi_1.22.5 > [13] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.3 BiocInstaller_1.10.1 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationForge_1.2.1 genefilter_1.42.0 grid_3.0.0 > [5] GSEABase_1.22.0 IRanges_1.18.0 lattice_0.20-15 RBGL_1.36.2 > [9] splines_3.0.0 stats4_3.0.0 survival_2.37-4 tools_3.0.0 > [13] XML_3.96-1.1 xtable_1.7-1 >> > [[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
ADD COMMENTlink written 5.9 years ago by Dan Tenenbaum8.2k
Answer: serious problem with GOstats package
0
gravatar for Steve Lianoglou
5.9 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Wed, May 8, 2013 at 8:38 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: > Hi, > > FOr my current analysis, I use GOstats package because it's a good, basic, simple package. > I don't know why but since some time , > > when I use this code: > > params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = universeGeneIds , ontology=onto, pvalueCutoff= 0.01,conditional=FALSE,testDirection="over") > > hgOver <- hyperGTest(params) > > I have this error message: > > > Erreur dans eapply(ID2GO(datPkg), function(goids) { : > erreur d'?valuation de l'argument 'env' lors de la s?lection d'une m?thode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable) : > unable to find an inherited method for function ?cols? for signature ?"function"? > > I have tested with R2.15.1, 2.12.! always the same problem. I think that the update of the package is sometimes problematic. I'm guessing that a problem with the package is unlikely seeing as how the vignette compiles (and recompiles almost nightly in devel(?)) just fine. My guess is that you are passing in some wonky params into the function and perhaps you should look a bit more closely at what the values of the geneIds, universeGeneIds, etc. are that you are sending to the function. -steve -- Steve Lianoglou Computational Biologist Department of Bioinformatics and Computational Biology Genentech
ADD COMMENTlink written 5.9 years ago by Steve Lianoglou12k
Answer: serious problem with GOstats package
0
gravatar for James W. MacDonald
5.9 years ago by
United States
James W. MacDonald49k wrote:
Hi Greg, On 5/8/2013 11:38 AM, gregory voisin wrote: > Hi,? > > FOr my current analysis, I use GOstats package because it's a good, basic, simple package. > I don't know why but since some time , > > when I use this code: > > params<- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = universeGeneIds , ontology=onto, pvalueCutoff= 0.01,conditional=FALSE,testDirection="over") You are missing the annotation argument. Best, Jim > ? > hgOver<- hyperGTest(params) > > I have this error message: > > > Erreur dans eapply(ID2GO(datPkg), function(goids) { :? > ? erreur d'??valuation de l'argument 'env' lors de la s??lection d'une m??thode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable) ? :? > ? unable to find an inherited method for function ???cols??? for signature ???"function"??? > > I have tested with R2.15.1, 2.12.! always the same problem. I think that the update of the package is sometimes problematic. > > > If you have a solution, a suggestion or an alternative ( I'm going to see topGO) > > ? > > Thanks for your help > > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=French_Canada.1252 ? LC_CTYPE=French_Canada.1252 ? ? LC_MONETARY=French_Canada.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? LC_TIME=French_Canada.1252 ? ? > > attached base packages: > [1] parallel ? stats ? ? graphics ? grDevices utils ? ? datasets ? methods ? base ? ? ? > > other attached packages: > ? [1] hgu95av2.db_2.9.0 ? ? org.Hs.eg.db_2.9.0 ? ALL_1.4.14 ? ? ? ? ? topGO_2.12.0 ? ? ? ? > ? [5] SparseM_0.99 ? ? ? ? GO.db_2.9.0 ? ? ? ? ? GOstats_2.26.0 ? ? ? RSQLite_0.11.3 ? ? ? > ? [9] DBI_0.2-6 ? ? ? ? ? ? graph_1.38.0 ? ? ? ? Category_2.26.0 ? ? ? AnnotationDbi_1.22.5 > [13] Biobase_2.20.0 ? ? ? BiocGenerics_0.6.0 ? limma_3.16.3 ? ? ? ? BiocInstaller_1.10.1 > > loaded via a namespace (and not attached): > ? [1] annotate_1.38.0 ? ? ? AnnotationForge_1.2.1 genefilter_1.42.0 ? ? grid_3.0.0 ? ? ? ? ? ? > ? [5] GSEABase_1.22.0 ? ? ? IRanges_1.18.0 ? ? ? ? lattice_0.20-15 ? ? ? RBGL_1.36.2 ? ? ? ? ? > ? [9] splines_3.0.0 ? ? ? ? stats4_3.0.0 ? ? ? ? ? survival_2.37-4 ? ? ? tools_3.0.0 ? ? ? ? ? > [13] XML_3.96-1.1 ? ? ? ? ? xtable_1.7-1 ? ? ? ? ? > [[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 5.9 years ago by James W. MacDonald49k
Answer: serious problem with GOstats package
0
gravatar for Dan Tenenbaum
5.9 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Thu, May 9, 2013 at 6:57 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: > HI Dan > > My feeling about this problem is perhaps a not appropriate use of Gostat. > > Currently , I use Gostats with a package .db for lumi or affy... > > In the present case, i use Agilent platform and I don't specify the package( > because it isn't existed) but I precise my geneUnivers. This approach is it > correct? Now, I'm not sure..I doubt > > Thanks for your help > I think James was right when he said you were missing the annotation argument? Dan > Greg > > > > > ________________________________ > De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > ? : gregory voisin <voisingreg at="" yahoo.fr=""> > Cc : bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Envoy? le : Mercredi 8 mai 2013 19h12 > Objet : Re: [BioC] serious problem with GOstats package > > Hi Gregory, > > > On Wed, May 8, 2013 at 8:38 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: >> Hi, >> >> FOr my current analysis, I use GOstats package because it's a good, basic, >> simple package. >> I don't know why but since some time , >> >> when I use this code: >> >> params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = >> universeGeneIds , ontology=onto, pvalueCutoff= >> 0.01,conditional=FALSE,testDirection="over") > > What are the values of sigLL, universeGeneIds, and onto? > > Please post a complete reproducible example. > > Thanks, > Dan > > >> >> hgOver <- hyperGTest(params) >> >> I have this error message: >> >> >> Erreur dans eapply(ID2GO(datPkg), function(goids) { : >> erreur d'?valuation de l'argument 'env' lors de la s?lection d'une >> m?thode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, >> mtable) : >> unable to find an inherited method for function ?cols? for signature >> ?"function"? >> >> I have tested with R2.15.1, 2.12.! always the same problem. I think that >> the update of the package is sometimes problematic. >> >> >> If you have a solution, a suggestion or an alternative ( I'm going to see >> topGO) >> >> >> >> Thanks for your help >> >> >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252 >> LC_MONETARY=French_Canada.1252 >> [4] LC_NUMERIC=C LC_TIME=French_Canada.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] hgu95av2.db_2.9.0 org.Hs.eg.db_2.9.0 ALL_1.4.14 >> topGO_2.12.0 >> [5] SparseM_0.99 GO.db_2.9.0 GOstats_2.26.0 >> RSQLite_0.11.3 >> [9] DBI_0.2-6 graph_1.38.0 Category_2.26.0 >> AnnotationDbi_1.22.5 >> [13] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.3 >> BiocInstaller_1.10.1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.38.0 AnnotationForge_1.2.1 genefilter_1.42.0 >> grid_3.0.0 >> [5] GSEABase_1.22.0 IRanges_1.18.0 lattice_0.20-15 >> RBGL_1.36.2 >> [9] splines_3.0.0 stats4_3.0.0 survival_2.37-4 >> tools_3.0.0 >> [13] XML_3.96-1.1 xtable_1.7-1 >>> >> [[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 >
ADD COMMENTlink written 5.9 years ago by Dan Tenenbaum8.2k
On 5/9/2013 10:29 AM, Dan Tenenbaum wrote: > On Thu, May 9, 2013 at 6:57 AM, gregory voisin<voisingreg at="" yahoo.fr=""> wrote: >> HI Dan >> >> My feeling about this problem is perhaps a not appropriate use of Gostat. >> >> Currently , I use Gostats with a package .db for lumi or affy... >> >> In the present case, i use Agilent platform and I don't specify the package( >> because it isn't existed) but I precise my geneUnivers. This approach is it >> correct? Now, I'm not sure..I doubt >> >> Thanks for your help >> > I think James was right when he said you were missing the annotation argument? And in the case where there isn't a chip-specific .db package, you use the org.Xx.eg.db package. IIRC, these are human, so it would be org.Hs.eg.db. Best, Jim > Dan > > >> Greg >> >> >> >> >> ________________________________ >> De : Dan Tenenbaum<dtenenba at="" fhcrc.org=""> >> ? : gregory voisin<voisingreg at="" yahoo.fr=""> >> Cc : bioconductor<bioconductor at="" stat.math.ethz.ch=""> >> Envoy? le : Mercredi 8 mai 2013 19h12 >> Objet : Re: [BioC] serious problem with GOstats package >> >> Hi Gregory, >> >> >> On Wed, May 8, 2013 at 8:38 AM, gregory voisin<voisingreg at="" yahoo.fr=""> wrote: >>> Hi, >>> >>> FOr my current analysis, I use GOstats package because it's a good, basic, >>> simple package. >>> I don't know why but since some time , >>> >>> when I use this code: >>> >>> params<- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = >>> universeGeneIds , ontology=onto, pvalueCutoff= >>> 0.01,conditional=FALSE,testDirection="over") >> What are the values of sigLL, universeGeneIds, and onto? >> >> Please post a complete reproducible example. >> >> Thanks, >> Dan >> >> >>> hgOver<- hyperGTest(params) >>> >>> I have this error message: >>> >>> >>> Erreur dans eapply(ID2GO(datPkg), function(goids) { : >>> erreur d'?valuation de l'argument 'env' lors de la s?lection d'une >>> m?thode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, >>> mtable) : >>> unable to find an inherited method for function ?cols? for signature >>> ?"function"? >>> >>> I have tested with R2.15.1, 2.12.! always the same problem. I think that >>> the update of the package is sometimes problematic. >>> >>> >>> If you have a solution, a suggestion or an alternative ( I'm going to see >>> topGO) >>> >>> >>> >>> Thanks for your help >>> >>> >>>> sessionInfo() >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252 >>> LC_MONETARY=French_Canada.1252 >>> [4] LC_NUMERIC=C LC_TIME=French_Canada.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] hgu95av2.db_2.9.0 org.Hs.eg.db_2.9.0 ALL_1.4.14 >>> topGO_2.12.0 >>> [5] SparseM_0.99 GO.db_2.9.0 GOstats_2.26.0 >>> RSQLite_0.11.3 >>> [9] DBI_0.2-6 graph_1.38.0 Category_2.26.0 >>> AnnotationDbi_1.22.5 >>> [13] Biobase_2.20.0 BiocGenerics_0.6.0 limma_3.16.3 >>> BiocInstaller_1.10.1 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.38.0 AnnotationForge_1.2.1 genefilter_1.42.0 >>> grid_3.0.0 >>> [5] GSEABase_1.22.0 IRanges_1.18.0 lattice_0.20-15 >>> RBGL_1.36.2 >>> [9] splines_3.0.0 stats4_3.0.0 survival_2.37-4 >>> tools_3.0.0 >>> [13] XML_3.96-1.1 xtable_1.7-1 >>> [[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 > _______________________________________________ > 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 REPLYlink written 5.9 years ago by James W. MacDonald49k
Answer: serious problem with GOstats package
0
gravatar for James W. MacDonald
5.9 years ago by
United States
James W. MacDonald49k wrote:
Hi Greg, It doesn't really matter what you think should happen, nor what the theory might be. What matters is how the code works and what the requirements are. In this case the code requires that you pass in an annotation package name, which is then used to map the Entrez Gene IDs to GO terms. You are expecting the GOstats package to take your Entrez Gene IDs and then somehow look them up and figure out what the species might be, against all evidence to the contrary. I suppose this could hypothetically be done, but that isn't how the code works. So if you look at the vignette, you will see this: params <- new("GOHyperGParams", + geneIds=selectedEntrezIds, + universeGeneIds=entrezUniverse, + annotation="hgu95av2.db", + ontology="BP", + pvalueCutoff=hgCutoff, + conditional=FALSE, + testDirection="over") Please note that both the universe AND the annotation package are included. Now if we delve into the code, we can see that one of the first steps in the hyperGTest function is to build the universe: > GOstats:::.hyperGTestInternal function (p) { p <- makeValidParams(p) p at universeGeneIds <- universeBuilder(p) and if we delve a bit deeper, we find this in the getUniverseViaGo function > getAnywhere(getUniverseViaGo) A single object matching ?getUniverseViaGo? was found It was found in the following places namespace:Category with value function (p) { datPkg <- p at datPkg ontology <- ontology(p) entrezIds <- universeGeneIds(p) ontology <- match.arg(ontology, c("BP", "CC", "MF")) ontIds <- aqListGOIDs(ontology) probe2go <- eapply(ID2GO(datPkg), function(goids) { Now that ^^^^^^^^ line looks pretty close to your error, no? So what exactly is p at datPkg? > showClass("GOHyperGParams") Class "GOHyperGParams" [package "Category"] Slots: Name: ontology conditional geneIds universeGeneIds Class: character logical ANY ANY Name: annotation datPkg categorySubsetIds categoryName Class: character DatPkg ANY character Name: pvalueCutoff testDirection Class: numeric character Extends: "HyperGParams" It's the annotation package name that you neglected to include when you built your GOHyperGParams object. And just to check, to make super sure I am right, > p <- new("GOHyperGParams", geneIds = "1", universeGeneIds = c("1","2","3"), annotation = "org.Hs.eg.db") > p at datPkg An object of class "Org.XX.egDatPkg" Slot "name": [1] "org.Hs.eg" So please try again, this time including the annotation package as I suggested before. Best, Jim On 5/9/2013 7:31 AM, gregory voisin wrote: > HI Jim, > > In my mind , in GO term analysis theory : two arguments are necessary > : the genelist selection and the genelistUnivers.^The annotation will > be necessary only if the universeGeneIds is absent. > After Gostats knows these submitted EntrezID are HUMAN but not the > experiement is based on Agilent platform. > Here , in this exemple : onto = "BP" > > > See a previous mail to Dan with a complete example of data and code. > > Thansk for your help > -------------------------------------------------------------------- ---- > *De :* James W. MacDonald <jmacdon at="" uw.edu=""> > *? :* gregory voisin <voisingreg at="" yahoo.fr=""> > *Cc :* bioconductor <bioconductor at="" stat.math.ethz.ch=""> > *Envoy? le :* Mercredi 8 mai 2013 19h19 > *Objet :* Re: [BioC] serious problem with GOstats package > > Hi Greg, > > On 5/8/2013 11:38 AM, gregory voisin wrote: > > Hi,? > > > > FOr my current analysis, I use GOstats package because it's a good, > basic, simple package. > > I don't know why but since some time , > > > > when I use this code: > > > > params<- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = > universeGeneIds , ontology=onto, pvalueCutoff= > 0.01,conditional=FALSE,testDirection="over") > > You are missing the annotation argument. > > Best, > > Jim > > > > ? > > hgOver<- hyperGTest(params) > > > > I have this error message: > > > > > > Erreur dans eapply(ID2GO(datPkg), function(goids) { :? > > ? erreur d'??valuation de l'argument 'env' lors de la s??lection > d'une m??thode pour la fonction 'eapply' : Erreur dans (function > (classes, fdef, mtable) ? :? > > ? unable to find an inherited method for function ???cols??? for > signature ???"function"??? > > > > I have tested with R2.15.1, 2.12.! always the same problem. I think > that the update of the package is sometimes problematic. > > > > > > If you have a solution, a suggestion or an alternative ( I'm going > to see topGO) > > > > ? > > > > Thanks for your help > > > > > >> sessionInfo() > > R version 3.0.0 (2013-04-03) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=French_Canada.1252 ? LC_CTYPE=French_Canada.1252 ? ? > LC_MONETARY=French_Canada.1252 > > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? > LC_TIME=French_Canada.1252 ? ? > > > > attached base packages: > > [1] parallel ? stats ? ? graphics ? grDevices utils ? ? datasets > ? methods ? base ? ? ? > > > > other attached packages: > > ? [1] hgu95av2.db_2.9.0 ? ? org.Hs.eg.db_2.9.0 ? ALL_1.4.14 ? ? > ? ? ? topGO_2.12.0 ? ? ? ? > > ? [5] SparseM_0.99 ? ? ? ? GO.db_2.9.0 ? ? ? ? ? > GOstats_2.26.0 ? ? ? RSQLite_0.11.3 ? ? ? > > ? [9] DBI_0.2-6 ? ? ? ? ? ? graph_1.38.0 ? ? ? ? > Category_2.26.0 ? ? ? AnnotationDbi_1.22.5 > > [13] Biobase_2.20.0 ? ? ? BiocGenerics_0.6.0 ? limma_3.16.3 ? > ? ? ? BiocInstaller_1.10.1 > > > > loaded via a namespace (and not attached): > > ? [1] annotate_1.38.0 ? ? ? AnnotationForge_1.2.1 > genefilter_1.42.0 ? ? grid_3.0.0 ? ? ? ? ? ? > > ? [5] GSEABase_1.22.0 ? ? ? IRanges_1.18.0 ? ? ? ? > lattice_0.20-15 ? ? ? RBGL_1.36.2 ? ? ? ? ? > > ? [9] splines_3.0.0 ? ? ? ? stats4_3.0.0 ? ? ? ? ? > survival_2.37-4 ? ? ? tools_3.0.0 ? ? ? ? ? > > [13] XML_3.96-1.1 ? ? ? ? ? xtable_1.7-1 ? ? ? ? ? > > [[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 COMMENTlink written 5.9 years ago by James W. MacDonald49k
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