Annotation packages
1
0
Entering edit mode
Sim, Fraser ▴ 350
@sim-fraser-2871
Last seen 7.4 years ago
Hi- I have a quick question relating to the use of annotation packages in Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E chips. I have performed RMA and generated expression data for each chip type individually and then used rbind to make a single matrix with all the data. I can use limma just fine to then perform differential gene analysis. I would like to use additional functions such as GO Hyper G testing but I couldn't find an annotation package that combined all 5 chips. How would I go about generating a new annotation package that combined the five individual annotation packages? Or how should I approach this problem? Thanks, Fraser SessionInfo: R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices datasets utils tools methods base other attached packages: [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 annaffy_1.12.1 KEGG.db_2.2.0 [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.9-3 GOstats_2.6.0 [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0 [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 graph_1.18.1 limma_2.14.5 [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 preprocessCore_1.2.0 affyio_1.8.0 [31] Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.10 XML_1.94-0.1 [[alternative HTML version deleted]]
Annotation GO hgu95av2 affy limma Annotation GO hgu95av2 affy limma • 962 views
ADD COMMENT
0
Entering edit mode
@sean-davis-490
Last seen 5 days ago
United States
On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser <fraser_sim at="" urmc.rochester.edu=""> wrote: > Hi- > > > > I have a quick question relating to the use of annotation packages in > Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E > chips. I have performed RMA and generated expression data for each chip > type individually and then used rbind to make a single matrix with all > the data. I can use limma just fine to then perform differential gene > analysis. > > > > I would like to use additional functions such as GO Hyper G testing but > I couldn't find an annotation package that combined all 5 chips. How > would I go about generating a new annotation package that combined the > five individual annotation packages? Or how should I approach this > problem? You can always build your own annotation package. The documentation is in the AnnotationDbi package. In particular, see the SQLForge vignette. Sean > SessionInfo: > > > > R version 2.7.0 (2008-04-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] splines stats graphics grDevices datasets utils tools > methods base > > > > other attached packages: > > [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 > gdata_2.4.2 gtools_2.5.0 > > [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 > annaffy_1.12.1 KEGG.db_2.2.0 > > [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 > RCurl_0.9-3 GOstats_2.6.0 > > [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > xtable_1.5-2 GO.db_2.2.0 > > [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > graph_1.18.1 limma_2.14.5 > > [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 > preprocessCore_1.2.0 affyio_1.8.0 > > [31] Biobase_2.0.1 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.10 XML_1.94-0.1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENT
0
Entering edit mode
I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > makeHUMANCHIP_DB(affy = FALSE, + prefix = "hgu95a-e2", + fileName = "extdata.txt", + baseMapType = "eg", + version = "1.0.0", + manufacturer = "Affymetrix", + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", + manufacturerUrl = "http://www.affymetrix.com") baseMapType is eg Prepending Metadata Creating Genes table Appending Probes Found 0 Probe Accessions Appending Gene Info Found 49221 Gene Names Found 49221 Gene Symbols Appending Chromosomes Appending Cytogenetic Locations Appending Omim Appending RefSeq Appending Pubmed Appending Unigene Appending ChrLengths Appending 3 GO tables Appending 3 GO ALL tables Appending KEGG Appending EC Appending Chromosome Locations Appending Pfam Appending Prosite Appending Alias Appending Ensembl Appending Metadata Creating package in ./hgu95a-e2.db > library("hgu95a-e2.db", lib.loc = getwd()) Error in library("hgu95a-e2.db", lib.loc = getwd()) : 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? Thanks, Fraser -----Original Message----- From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Thursday, October 30, 2008 4:19 PM To: Sim, Fraser Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Annotation packages On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser <fraser_sim at="" urmc.rochester.edu=""> wrote: > Hi- > > > > I have a quick question relating to the use of annotation packages in > Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E > chips. I have performed RMA and generated expression data for each chip > type individually and then used rbind to make a single matrix with all > the data. I can use limma just fine to then perform differential gene > analysis. > > > > I would like to use additional functions such as GO Hyper G testing but > I couldn't find an annotation package that combined all 5 chips. How > would I go about generating a new annotation package that combined the > five individual annotation packages? Or how should I approach this > problem? You can always build your own annotation package. The documentation is in the AnnotationDbi package. In particular, see the SQLForge vignette. Sean > SessionInfo: > > > > R version 2.7.0 (2008-04-22) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] splines stats graphics grDevices datasets utils tools > methods base > > > > other attached packages: > > [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 > gdata_2.4.2 gtools_2.5.0 > > [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 > annaffy_1.12.1 KEGG.db_2.2.0 > > [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 > RCurl_0.9-3 GOstats_2.6.0 > > [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > xtable_1.5-2 GO.db_2.2.0 > > [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > graph_1.18.1 limma_2.14.5 > > [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 > preprocessCore_1.2.0 affyio_1.8.0 > > [31] Biobase_2.0.1 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.10 XML_1.94-0.1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY
0
Entering edit mode
Hi Fraser, Did you R CMD INSTALL the package that you made? SQLForge will produce the source code for the package you want, but you need to then use R to build or install it. You cannot just call library to try and load it without even leaving the session which is what your post seems to suggest. Also can you show us your sessionInfo()? Marc Sim, Fraser wrote: > I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > > >> makeHUMANCHIP_DB(affy = FALSE, >> > + prefix = "hgu95a-e2", > + fileName = "extdata.txt", > + baseMapType = "eg", > + version = "1.0.0", > + manufacturer = "Affymetrix", > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > + manufacturerUrl = "http://www.affymetrix.com") > baseMapType is eg > Prepending Metadata > Creating Genes table > Appending Probes > Found 0 Probe Accessions > Appending Gene Info > Found 49221 Gene Names > Found 49221 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Metadata > > > Creating package in ./hgu95a-e2.db > > >> library("hgu95a-e2.db", lib.loc = getwd()) >> > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > Thanks, > Fraser > > -----Original Message----- > From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis > Sent: Thursday, October 30, 2008 4:19 PM > To: Sim, Fraser > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > <fraser_sim at="" urmc.rochester.edu=""> wrote: > >> Hi- >> >> >> >> I have a quick question relating to the use of annotation packages in >> Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E >> chips. I have performed RMA and generated expression data for each chip >> type individually and then used rbind to make a single matrix with all >> the data. I can use limma just fine to then perform differential gene >> analysis. >> >> >> >> I would like to use additional functions such as GO Hyper G testing but >> I couldn't find an annotation package that combined all 5 chips. How >> would I go about generating a new annotation package that combined the >> five individual annotation packages? Or how should I approach this >> problem? >> > > You can always build your own annotation package. The documentation > is in the AnnotationDbi package. In particular, see the SQLForge > vignette. > > Sean > > >> SessionInfo: >> >> >> >> R version 2.7.0 (2008-04-22) >> >> i386-pc-mingw32 >> >> >> >> locale: >> >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> >> >> attached base packages: >> >> [1] splines stats graphics grDevices datasets utils tools >> methods base >> >> >> >> other attached packages: >> >> [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 >> gdata_2.4.2 gtools_2.5.0 >> >> [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 >> annaffy_1.12.1 KEGG.db_2.2.0 >> >> [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 >> RCurl_0.9-3 GOstats_2.6.0 >> >> [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 >> xtable_1.5-2 GO.db_2.2.0 >> >> [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 >> graph_1.18.1 limma_2.14.5 >> >> [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 >> preprocessCore_1.2.0 affyio_1.8.0 >> >> [31] Biobase_2.0.1 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] cluster_1.11.10 XML_1.94-0.1 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLY
0
Entering edit mode
Hi Marc, My sessionInfo is at the end of the original email. How do I use R CMD INSTALL? I am on WindowsXP and it looks like something I'd need Linux to use. Thanks, Fraser -----Original Message----- From: Marc Carlson [mailto:mcarlson@fhcrc.org] Sent: Thursday, October 30, 2008 5:51 PM To: Sim, Fraser Cc: Sean Davis; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Annotation packages Hi Fraser, Did you R CMD INSTALL the package that you made? SQLForge will produce the source code for the package you want, but you need to then use R to build or install it. You cannot just call library to try and load it without even leaving the session which is what your post seems to suggest. Also can you show us your sessionInfo()? Marc Sim, Fraser wrote: > I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > > >> makeHUMANCHIP_DB(affy = FALSE, >> > + prefix = "hgu95a-e2", > + fileName = "extdata.txt", > + baseMapType = "eg", > + version = "1.0.0", > + manufacturer = "Affymetrix", > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > + manufacturerUrl = "http://www.affymetrix.com") > baseMapType is eg > Prepending Metadata > Creating Genes table > Appending Probes > Found 0 Probe Accessions > Appending Gene Info > Found 49221 Gene Names > Found 49221 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Metadata > > > Creating package in ./hgu95a-e2.db > > >> library("hgu95a-e2.db", lib.loc = getwd()) >> > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > Thanks, > Fraser > > -----Original Message----- > From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis > Sent: Thursday, October 30, 2008 4:19 PM > To: Sim, Fraser > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > <fraser_sim at="" urmc.rochester.edu=""> wrote: > >> Hi- >> >> >> >> I have a quick question relating to the use of annotation packages in >> Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E >> chips. I have performed RMA and generated expression data for each chip >> type individually and then used rbind to make a single matrix with all >> the data. I can use limma just fine to then perform differential gene >> analysis. >> >> >> >> I would like to use additional functions such as GO Hyper G testing but >> I couldn't find an annotation package that combined all 5 chips. How >> would I go about generating a new annotation package that combined the >> five individual annotation packages? Or how should I approach this >> problem? >> > > You can always build your own annotation package. The documentation > is in the AnnotationDbi package. In particular, see the SQLForge > vignette. > > Sean > > >> SessionInfo: >> >> >> >> R version 2.7.0 (2008-04-22) >> >> i386-pc-mingw32 >> >> >> >> locale: >> >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> >> >> attached base packages: >> >> [1] splines stats graphics grDevices datasets utils tools >> methods base >> >> >> >> other attached packages: >> >> [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 >> gdata_2.4.2 gtools_2.5.0 >> >> [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 >> annaffy_1.12.1 KEGG.db_2.2.0 >> >> [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 >> RCurl_0.9-3 GOstats_2.6.0 >> >> [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 >> xtable_1.5-2 GO.db_2.2.0 >> >> [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 >> graph_1.18.1 limma_2.14.5 >> >> [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 >> preprocessCore_1.2.0 affyio_1.8.0 >> >> [31] Biobase_2.0.1 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] cluster_1.11.10 XML_1.94-0.1 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLY
0
Entering edit mode
On Fri, Oct 31, 2008 at 11:21 AM, Sim, Fraser <fraser_sim@urmc.rochester.edu> wrote: > Hi Marc, > > My sessionInfo is at the end of the original email. > > How do I use R CMD INSTALL? I am on WindowsXP and it looks like > something I'd need Linux to use? You'll need to install RTools. See the R-for-windows FAQ for details. Sean > > -----Original Message----- > From: Marc Carlson [mailto:mcarlson@fhcrc.org] > Sent: Thursday, October 30, 2008 5:51 PM > To: Sim, Fraser > Cc: Sean Davis; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > Hi Fraser, > > Did you R CMD INSTALL the package that you made? SQLForge will produce > the source code for the package you want, but you need to then use R to > build or install it. You cannot just call library to try and load it > without even leaving the session which is what your post seems to > suggest. Also can you show us your sessionInfo()? > > > Marc > > > > > Sim, Fraser wrote: > > I tried to follow the instructions. I thought it had successfully made > an annotation package but I can't load it. See code and results below. > The error says it is not a valid package. Any ideas? > > > > > >> makeHUMANCHIP_DB(affy = FALSE, > >> > > + prefix = "hgu95a-e2", > > + fileName = "extdata.txt", > > + baseMapType = "eg", > > + version = "1.0.0", > > + manufacturer = "Affymetrix", > > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > > + manufacturerUrl = "http://www.affymetrix.com") > > baseMapType is eg > > Prepending Metadata > > Creating Genes table > > Appending Probes > > Found 0 Probe Accessions > > Appending Gene Info > > Found 49221 Gene Names > > Found 49221 Gene Symbols > > Appending Chromosomes > > Appending Cytogenetic Locations > > Appending Omim > > Appending RefSeq > > Appending Pubmed > > Appending Unigene > > Appending ChrLengths > > Appending 3 GO tables > > Appending 3 GO ALL tables > > Appending KEGG > > Appending EC > > Appending Chromosome Locations > > Appending Pfam > > Appending Prosite > > Appending Alias > > Appending Ensembl > > Appending Metadata > > > > > > Creating package in ./hgu95a-e2.db > > > > > >> library("hgu95a-e2.db", lib.loc = getwd()) > >> > > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > > > Thanks, > > Fraser > > > > -----Original Message----- > > From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean > Davis > > Sent: Thursday, October 30, 2008 4:19 PM > > To: Sim, Fraser > > Cc: bioconductor@stat.math.ethz.ch > > Subject: Re: [BioC] Annotation packages > > > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > > <fraser_sim@urmc.rochester.edu> wrote: > > > >> Hi- > >> > >> > >> > >> I have a quick question relating to the use of annotation packages in > >> Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, > E > >> chips. I have performed RMA and generated expression data for each > chip > >> type individually and then used rbind to make a single matrix with > all > >> the data. I can use limma just fine to then perform differential gene > >> analysis. > >> > >> > >> > >> I would like to use additional functions such as GO Hyper G testing > but > >> I couldn't find an annotation package that combined all 5 chips. How > >> would I go about generating a new annotation package that combined > the > >> five individual annotation packages? Or how should I approach this > >> problem? > >> > > > > You can always build your own annotation package. The documentation > > is in the AnnotationDbi package. In particular, see the SQLForge > > vignette. > > > > Sean > > > > > >> SessionInfo: > >> > >> > >> > >> R version 2.7.0 (2008-04-22) > >> > >> i386-pc-mingw32 > >> > >> > >> > >> locale: > >> > >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > >> States.1252;LC_MONETARY=English_United > >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >> > >> > >> > >> attached base packages: > >> > >> [1] splines stats graphics grDevices datasets utils tools > >> methods base > >> > >> > >> > >> other attached packages: > >> > >> [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 > >> gdata_2.4.2 gtools_2.5.0 > >> > >> [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 > >> annaffy_1.12.1 KEGG.db_2.2.0 > >> > >> [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 > >> RCurl_0.9-3 GOstats_2.6.0 > >> > >> [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > >> xtable_1.5-2 GO.db_2.2.0 > >> > >> [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > >> graph_1.18.1 limma_2.14.5 > >> > >> [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 > >> preprocessCore_1.2.0 affyio_1.8.0 > >> > >> [31] Biobase_2.0.1 > >> > >> > >> > >> loaded via a namespace (and not attached): > >> > >> [1] cluster_1.11.10 XML_1.94-0.1 > >> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Hi Sean- Thanks. I guess what’s not very clear is how to do that in the documentation. Here’s how I did it in case other new users need more help. Install RTools from http://www.murdoch-sutherland.com/Rtools/ Open a cmd prompt (Start -> Run -> cmd.exe) Go to your program files folder and find the R installation folder. Go to the bin directory. Type Rcmd.exe INSTALL pkgname (Note: remember to use escape the backslash as in “\\” as otherwise R will parse the pkgname path incorrectly.) Hope that helps. My new annotation package installed just fine. I’ll use this technique to help out another lab member working with a custom eArray. Cheers, Fraser From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Friday, October 31, 2008 11:25 AM To: Sim, Fraser Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Annotation packages On Fri, Oct 31, 2008 at 11:21 AM, Sim, Fraser <fraser_sim@urmc.rochester.edu> wrote: Hi Marc, My sessionInfo is at the end of the original email. How do I use R CMD INSTALL? I am on WindowsXP and it looks like something I'd need Linux to use? You'll need to install RTools. See the R-for-windows FAQ for details. Sean -----Original Message----- From: Marc Carlson [mailto:mcarlson@fhcrc.org] Sent: Thursday, October 30, 2008 5:51 PM To: Sim, Fraser Cc: Sean Davis; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Annotation packages Hi Fraser, Did you R CMD INSTALL the package that you made? SQLForge will produce the source code for the package you want, but you need to then use R to build or install it. You cannot just call library to try and load it without even leaving the session which is what your post seems to suggest. Also can you show us your sessionInfo()? Marc Sim, Fraser wrote: > I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > > >> makeHUMANCHIP_DB(affy = FALSE, >> > + prefix = "hgu95a-e2", > + fileName = "extdata.txt", > + baseMapType = "eg", > + version = "1.0.0", > + manufacturer = "Affymetrix", > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > + manufacturerUrl = "http://www.affymetrix.com") > baseMapType is eg > Prepending Metadata > Creating Genes table > Appending Probes > Found 0 Probe Accessions > Appending Gene Info > Found 49221 Gene Names > Found 49221 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Metadata > > > Creating package in ./hgu95a-e2.db > > >> library("hgu95a-e2.db", lib.loc = getwd()) >> > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > Thanks, > Fraser > > -----Original Message----- > From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis > Sent: Thursday, October 30, 2008 4:19 PM > To: Sim, Fraser > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > <fraser_sim@urmc.rochester.edu> wrote: > >> Hi- >> >> >> >> I have a quick question relating to the use of annotation packages in >> Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E >> chips. I have performed RMA and generated expression data for each chip >> type individually and then used rbind to make a single matrix with all >> the data. I can use limma just fine to then perform differential gene >> analysis. >> >> >> >> I would like to use additional functions such as GO Hyper G testing but >> I couldn't find an annotation package that combined all 5 chips. How >> would I go about generating a new annotation package that combined the >> five individual annotation packages? Or how should I approach this >> problem? >> > > You can always build your own annotation package. The documentation > is in the AnnotationDbi package. In particular, see the SQLForge > vignette. > > Sean > > >> SessionInfo: >> >> >> >> R version 2.7.0 (2008-04-22) >> >> i386-pc-mingw32 >> >> >> >> locale: >> >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> >> >> attached base packages: >> >> [1] splines stats graphics grDevices datasets utils tools >> methods base >> >> >> >> other attached packages: >> >> [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 >> gdata_2.4.2 gtools_2.5.0 >> >> [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 >> annaffy_1.12.1 KEGG.db_2.2.0 >> >> [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 >> RCurl_0.9-3 GOstats_2.6.0 >> >> [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 >> xtable_1.5-2 GO.db_2.2.0 >> >> [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 >> graph_1.18.1 limma_2.14.5 >> >> [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 >> preprocessCore_1.2.0 affyio_1.8.0 >> >> [31] Biobase_2.0.1 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] cluster_1.11.10 XML_1.94-0.1 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
"-" might not be a valid character for package names (or I'd remember it did not use to be) L. On Thu, 2008-10-30 at 17:12 -0400, Sim, Fraser wrote: > I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > > > makeHUMANCHIP_DB(affy = FALSE, > + prefix = "hgu95a-e2", > + fileName = "extdata.txt", > + baseMapType = "eg", > + version = "1.0.0", > + manufacturer = "Affymetrix", > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > + manufacturerUrl = "http://www.affymetrix.com") > baseMapType is eg > Prepending Metadata > Creating Genes table > Appending Probes > Found 0 Probe Accessions > Appending Gene Info > Found 49221 Gene Names > Found 49221 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Metadata > > > Creating package in ./hgu95a-e2.db > > > library("hgu95a-e2.db", lib.loc = getwd()) > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > Thanks, > Fraser > > -----Original Message----- > From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis > Sent: Thursday, October 30, 2008 4:19 PM > To: Sim, Fraser > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > <fraser_sim at="" urmc.rochester.edu=""> wrote: > > Hi- > > > > > > > > I have a quick question relating to the use of annotation packages in > > Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E > > chips. I have performed RMA and generated expression data for each chip > > type individually and then used rbind to make a single matrix with all > > the data. I can use limma just fine to then perform differential gene > > analysis. > > > > > > > > I would like to use additional functions such as GO Hyper G testing but > > I couldn't find an annotation package that combined all 5 chips. How > > would I go about generating a new annotation package that combined the > > five individual annotation packages? Or how should I approach this > > problem? > > You can always build your own annotation package. The documentation > is in the AnnotationDbi package. In particular, see the SQLForge > vignette. > > Sean > > > SessionInfo: > > > > > > > > R version 2.7.0 (2008-04-22) > > > > i386-pc-mingw32 > > > > > > > > locale: > > > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > > States.1252;LC_MONETARY=English_United > > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > > > > > attached base packages: > > > > [1] splines stats graphics grDevices datasets utils tools > > methods base > > > > > > > > other attached packages: > > > > [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 > > gdata_2.4.2 gtools_2.5.0 > > > > [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 > > annaffy_1.12.1 KEGG.db_2.2.0 > > > > [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 > > RCurl_0.9-3 GOstats_2.6.0 > > > > [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > > xtable_1.5-2 GO.db_2.2.0 > > > > [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > > graph_1.18.1 limma_2.14.5 > > > > [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 > > preprocessCore_1.2.0 affyio_1.8.0 > > > > [31] Biobase_2.0.1 > > > > > > > > loaded via a namespace (and not attached): > > > > [1] cluster_1.11.10 XML_1.94-0.1 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY
0
Entering edit mode
Thanks. I tried to repeat ommiting the "-" but got the same error message. -----Original Message----- From: laurent [mailto:lgautier@gmail.com] Sent: Thursday, October 30, 2008 5:21 PM To: Sim, Fraser Cc: Sean Davis; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Annotation packages "-" might not be a valid character for package names (or I'd remember it did not use to be) L. On Thu, 2008-10-30 at 17:12 -0400, Sim, Fraser wrote: > I tried to follow the instructions. I thought it had successfully made an annotation package but I can't load it. See code and results below. The error says it is not a valid package. Any ideas? > > > makeHUMANCHIP_DB(affy = FALSE, > + prefix = "hgu95a-e2", > + fileName = "extdata.txt", > + baseMapType = "eg", > + version = "1.0.0", > + manufacturer = "Affymetrix", > + chipName = "hgu95a,hgu95b,hgu95c,hgu95d,hgu95e", > + manufacturerUrl = "http://www.affymetrix.com") > baseMapType is eg > Prepending Metadata > Creating Genes table > Appending Probes > Found 0 Probe Accessions > Appending Gene Info > Found 49221 Gene Names > Found 49221 Gene Symbols > Appending Chromosomes > Appending Cytogenetic Locations > Appending Omim > Appending RefSeq > Appending Pubmed > Appending Unigene > Appending ChrLengths > Appending 3 GO tables > Appending 3 GO ALL tables > Appending KEGG > Appending EC > Appending Chromosome Locations > Appending Pfam > Appending Prosite > Appending Alias > Appending Ensembl > Appending Metadata > > > Creating package in ./hgu95a-e2.db > > > library("hgu95a-e2.db", lib.loc = getwd()) > Error in library("hgu95a-e2.db", lib.loc = getwd()) : > 'hgu95a-e2.db' is not a valid package -- installed < 2.0.0? > > Thanks, > Fraser > > -----Original Message----- > From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis > Sent: Thursday, October 30, 2008 4:19 PM > To: Sim, Fraser > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Annotation packages > > On Thu, Oct 30, 2008 at 4:12 PM, Sim, Fraser > <fraser_sim at="" urmc.rochester.edu=""> wrote: > > Hi- > > > > > > > > I have a quick question relating to the use of annotation packages in > > Bioconductor. I'm analyzing data from Affy arrays, the U95A, B, C, D, E > > chips. I have performed RMA and generated expression data for each chip > > type individually and then used rbind to make a single matrix with all > > the data. I can use limma just fine to then perform differential gene > > analysis. > > > > > > > > I would like to use additional functions such as GO Hyper G testing but > > I couldn't find an annotation package that combined all 5 chips. How > > would I go about generating a new annotation package that combined the > > five individual annotation packages? Or how should I approach this > > problem? > > You can always build your own annotation package. The documentation > is in the AnnotationDbi package. In particular, see the SQLForge > vignette. > > Sean > > > SessionInfo: > > > > > > > > R version 2.7.0 (2008-04-22) > > > > i386-pc-mingw32 > > > > > > > > locale: > > > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > > States.1252;LC_MONETARY=English_United > > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > > > > > attached base packages: > > > > [1] splines stats graphics grDevices datasets utils tools > > methods base > > > > > > > > other attached packages: > > > > [1] hgu95av2.db_2.2.0 bioDist_1.12.0 gplots_2.6.0 > > gdata_2.4.2 gtools_2.5.0 > > > > [6] RColorBrewer_1.0-2 RODBC_1.2-3 affycoretools_1.12.0 > > annaffy_1.12.1 KEGG.db_2.2.0 > > > > [11] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0 > > RCurl_0.9-3 GOstats_2.6.0 > > > > [16] Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 > > xtable_1.5-2 GO.db_2.2.0 > > > > [21] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 > > graph_1.18.1 limma_2.14.5 > > > > [26] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 > > preprocessCore_1.2.0 affyio_1.8.0 > > > > [31] Biobase_2.0.1 > > > > > > > > loaded via a namespace (and not attached): > > > > [1] cluster_1.11.10 XML_1.94-0.1 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY

Login before adding your answer.

Traffic: 492 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6