Question: Possible problem with Rhesus array annotation package
0
gravatar for blockaa@huskers.unl.edu
8.0 years ago by
Hello BioConductor list, I am fairly new to BioConductor. I am working with Affymetrix GeneChip Rhesus Macaque Genome Array. I am able to analysis my data, but I am not able to annotate the results using annaffy and annotate. I am using org.Mmu.eg.db as the annotation package. Part of the package seems to be missing. I am able to annotate a human array, so I don't think it is my code. My code (after analysis) is: > library("annaffy") > library("annotate") > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("org.Mmu.eg.db") Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "org.Mmu.eg.db" Please wait... Installing package(s) into ‘C:/Users/Andrew Block/Documents/R/win- library/2.13’ (as ‘lib’ is unspecified) trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin/w indows/contrib/2.13/org.Mmu.eg.db_2.5.0.zip' Content type 'application/zip' length 17734284 bytes (16.9 Mb) opened URL downloaded 16.9 Mb package 'org.Mmu.eg.db' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Andrew Block\AppData\Local\Temp\Rtmp36zrGk\downloaded_packages > library("org.Mmu.eg.db") > genenames <- as.character(toptable$ID) > atab <- aafTableAnn(genenames, "org.Mmu.eg.db", aaf.handler()) Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) : object 'org.Mmu.egORGPKG' not found In addition: Warning message: In chkPkgs(chip) : The org.Mmu.eg.db package does not appear to contain annotation data. > traceback() 5: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) 4: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) 3: aafGO(probeids, chip) 2: aaf.handler(probeids, chip, colnames[i]) 1: aafTableAnn(genenames1, "org.Mmu.eg.db", aaf.handler()) > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Mmu.eg.db_2.5.0 annotate_1.30.0 annaffy_1.24.0 [4] KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4 [7] DBI_0.2-5 AnnotationDbi_1.14.1 rhesuscdf_2.8.0 [10] limma_3.8.2 affy_1.30.0 Biobase_2.12.1 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.0 [4] xtable_1.5-6 Thank you for the help in advance. Andrew Block Nebraska Center of Virology University of Nebraska at Lincoln [[alternative HTML version deleted]]
annotation go annotate annaffy • 635 views
ADD COMMENTlink modified 8.0 years ago by Marc Carlson7.2k • written 8.0 years ago by blockaa@huskers.unl.edu30
Answer: Possible problem with Rhesus array annotation package
0
gravatar for Marc Carlson
8.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Andrew, I am not completely sure why aafGO() is claiming otherwise, but there definitely *is* data in the Mmu organism package. In a pinch, you can always access it generically with simple operations like this: library("org.Mmu.eg.db") ## lets make a feke top table for illustration purposes tt <- data.frame(gene_id = c("574097", "574098", "574099"), value= c(1:3)) tt ## now suppose that we want to attach the pubmed IDs to that. ## We could just attach it using merge() and the PMID mapping for rhesus just like this merge(tt, toTable(org.Mmu.egPMID), by.x="gene_id", by.y="gene_id") Hope this helps, Marc On 07/20/2011 01:51 PM, blockaa@huskers.unl.edu wrote: > Hello BioConductor list, > > > I am fairly new to BioConductor. I am working with Affymetrix GeneChip Rhesus Macaque Genome Array. I am able to analysis my data, but I am not able to annotate the results using annaffy and annotate. I am using org.Mmu.eg.db as the annotation package. Part of the package seems to be missing. I am able to annotate a human array, so I don't think it is my code. My code (after analysis) is: > > >> library("annaffy") >> library("annotate") >> source("http://www.bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > > Change using chooseBioCmirror(). > >> biocLite("org.Mmu.eg.db") > Using R version 2.13.0, biocinstall version 2.8.4. > > Installing Bioconductor version 2.8 packages: > > [1] "org.Mmu.eg.db" > > Please wait... > > > Installing package(s) into 'C:/Users/Andrew Block/Documents/R/win- library/2.13' > > (as 'lib' is unspecified) > > trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin /windows/contrib/2.13/org.Mmu.eg.db_2.5.0.zip' > > Content type 'application/zip' length 17734284 bytes (16.9 Mb) > > opened URL > > downloaded 16.9 Mb > > > package 'org.Mmu.eg.db' successfully unpacked and MD5 sums checked > > > The downloaded packages are in > > C:\Users\Andrew Block\AppData\Local\Temp\Rtmp36zrGk\downloaded_packages > >> library("org.Mmu.eg.db") > >> genenames<- as.character(toptable$ID) >> atab<- aafTableAnn(genenames, "org.Mmu.eg.db", aaf.handler()) > Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) : > > object 'org.Mmu.egORGPKG' not found > > In addition: Warning message: > > In chkPkgs(chip) : > > The org.Mmu.eg.db package does not appear to contain annotation data. > > >> traceback() > 5: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) > > 4: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) > > 3: aafGO(probeids, chip) > > 2: aaf.handler(probeids, chip, colnames[i]) > > 1: aafTableAnn(genenames1, "org.Mmu.eg.db", aaf.handler()) > > >> sessionInfo() > R version 2.13.0 (2011-04-13) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > > [1] org.Mmu.eg.db_2.5.0 annotate_1.30.0 annaffy_1.24.0 > > [4] KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4 > > [7] DBI_0.2-5 AnnotationDbi_1.14.1 rhesuscdf_2.8.0 > > [10] limma_3.8.2 affy_1.30.0 Biobase_2.12.1 > > > loaded via a namespace (and not attached): > > [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.0 > > [4] xtable_1.5-6 > > > Thank you for the help in advance. > > Andrew Block > > Nebraska Center of Virology > University of Nebraska at Lincoln > > [[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 COMMENTlink written 8.0 years ago by Marc Carlson7.2k
Hi Andrew, On closer examination this problem is because certain kinds of information are being search for by annaffy that are just not available for org.Mmu.eg.db. The kinds of information being searched for that are not found are: ENTREZID (this is actually present but is failing the check because this information is normally called "EG" in all of the org style packages), MAP and UNIGENE. The annaffy software is performing a check and then when it does not find these kinds of annotation if throws the error message that you observed. So there is nothing actually wrong with the annotations, they just don't contain certain specific kinds of data (that annaffy was expecting to find). Marc On 07/21/2011 03:02 PM, Marc Carlson wrote: > Hi Andrew, > > I am not completely sure why aafGO() is claiming otherwise, but there > definitely *is* data in the Mmu organism package. In a pinch, you can > always access it generically with simple operations like this: > > library("org.Mmu.eg.db") > ## lets make a feke top table for illustration purposes > tt<- data.frame(gene_id = c("574097", "574098", "574099"), value= c(1:3)) > tt > > ## now suppose that we want to attach the pubmed IDs to that. > ## We could just attach it using merge() and the PMID mapping for rhesus > just like this > > merge(tt, toTable(org.Mmu.egPMID), by.x="gene_id", by.y="gene_id") > > > Hope this helps, > > > Marc > > > > On 07/20/2011 01:51 PM, blockaa at huskers.unl.edu wrote: >> Hello BioConductor list, >> >> >> I am fairly new to BioConductor. I am working with Affymetrix GeneChip Rhesus Macaque Genome Array. I am able to analysis my data, but I am not able to annotate the results using annaffy and annotate. I am using org.Mmu.eg.db as the annotation package. Part of the package seems to be missing. I am able to annotate a human array, so I don't think it is my code. My code (after analysis) is: >> >> >>> library("annaffy") >>> library("annotate") >>> source("http://www.bioconductor.org/biocLite.R") >> BioC_mirror = http://bioconductor.org >> >> Change using chooseBioCmirror(). >> >>> biocLite("org.Mmu.eg.db") >> Using R version 2.13.0, biocinstall version 2.8.4. >> >> Installing Bioconductor version 2.8 packages: >> >> [1] "org.Mmu.eg.db" >> >> Please wait... >> >> >> Installing package(s) into 'C:/Users/Andrew Block/Documents/R/win- library/2.13' >> >> (as 'lib' is unspecified) >> >> trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bi n/windows/contrib/2.13/org.Mmu.eg.db_2.5.0.zip' >> >> Content type 'application/zip' length 17734284 bytes (16.9 Mb) >> >> opened URL >> >> downloaded 16.9 Mb >> >> >> package 'org.Mmu.eg.db' successfully unpacked and MD5 sums checked >> >> >> The downloaded packages are in >> >> C:\Users\Andrew Block\AppData\Local\Temp\Rtmp36zrGk\downloaded_packages >> >>> library("org.Mmu.eg.db") >>> genenames<- as.character(toptable$ID) >>> atab<- aafTableAnn(genenames, "org.Mmu.eg.db", aaf.handler()) >> Error in get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) : >> >> object 'org.Mmu.egORGPKG' not found >> >> In addition: Warning message: >> >> In chkPkgs(chip) : >> >> The org.Mmu.eg.db package does not appear to contain annotation data. >> >> >>> traceback() >> 5: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) >> >> 4: get(paste(gsub(".db", "", chip), "ORGPKG", sep = "")) >> >> 3: aafGO(probeids, chip) >> >> 2: aaf.handler(probeids, chip, colnames[i]) >> >> 1: aafTableAnn(genenames1, "org.Mmu.eg.db", aaf.handler()) >> >> >>> sessionInfo() >> R version 2.13.0 (2011-04-13) >> >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> >> attached base packages: >> >> [1] stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> >> [1] org.Mmu.eg.db_2.5.0 annotate_1.30.0 annaffy_1.24.0 >> >> [4] KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4 >> >> [7] DBI_0.2-5 AnnotationDbi_1.14.1 rhesuscdf_2.8.0 >> >> [10] limma_3.8.2 affy_1.30.0 Biobase_2.12.1 >> >> >> loaded via a namespace (and not attached): >> >> [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.0 >> >> [4] xtable_1.5-6 >> >> >> Thank you for the help in advance. >> >> Andrew Block >> >> Nebraska Center of Virology >> University of Nebraska at Lincoln >> >> [[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 > > [[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 REPLYlink written 8.0 years ago by Marc Carlson7.2k
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