Dear Bioconductor community, I just started working with the drosgenome1 environment. When I try to get the gene names from drosgenome1GENENAME, I only get 5 gene names and 14005 NA values. > table(GN) GN Fas (TNF receptor superfamily member) 1 FBJ murine osteosarcoma viral oncogene homolog 1 interleukin 10 1 interleukin 2 1 interleukin 4 1 NA 14005 A couple of other environments seem to be empty (SUMFUNC, PATH ...) Is that normal? Many thanks in advance for your comments, Emmanuel > sessionInfo() R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: drosgenome1 drosgenome1cdf annotate annaffy KEGG "1.10.0" "1.10.0" "1.8.0" "1.2.0" "1.8.1" GO affy Biobase "1.8.2" "1.8.1" "1.8.0" ===================================== drosgenome1 INSTALL INFO > biocLite("drosgenome1") Running bioCLite version 0.1 with R version 2.2.1 Running biocinstall version 1.1 with R version 2.2.1 trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7/s rc/contrib/drosgenome1_1.10.0.tar.gz' Content type 'application/x-gzip' length 3374185 bytes opened URL ================================================== downloaded 3295Kb * Installing *source* package 'drosgenome1' ... ** R ** data ** moving datasets to lazyload DB ** help >>> Building/Updating help pages for package 'drosgenome1' Formats: text html latex example drosgenome1 text html latex drosgenome1ACCNUM text html latex example drosgenome1CHR text html latex example drosgenome1CHRLOC text html latex example drosgenome1ENZYME text html latex example drosgenome1GENENAME text html latex example drosgenome1GO text html latex example drosgenome1GO2ALLPROBES text html latex example drosgenome1GO2PROBE text html latex example drosgenome1LOCUSID text html latex example drosgenome1MAP text html latex example drosgenome1ORGANISM text html latex example drosgenome1PATH text html latex example drosgenome1PMID text html latex example drosgenome1PMID2PROBE text html latex example drosgenome1QC text html latex drosgenome1REFSEQ text html latex example drosgenome1SUMFUNC text html latex example drosgenome1SYMBOL text html latex example drosgenome1UNIGENE text html latex example ** building package indices ... * DONE (drosgenome1) The downloaded packages are in /tmp/RtmpU18540/downloaded_packages

Hi Emmanuel, Thanks for reporting this problem. I will fix it in the coming release. Sincerely, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Thu, 23 Mar 2006, Emmanuel Levy wrote: > Dear Bioconductor community, > > I just started working with the drosgenome1 environment. > When I try to get the gene names from drosgenome1GENENAME, > I only get 5 gene names and 14005 NA values. > > > table(GN) > GN > Fas (TNF receptor superfamily member) > 1 > FBJ murine osteosarcoma viral oncogene homolog > 1 > interleukin 10 > 1 > interleukin 2 > 1 > interleukin 4 > 1 > NA > 14005 > > A couple of other environments seem to be empty (SUMFUNC, PATH ...) > > Is that normal? > > Many thanks in advance for your comments, > > Emmanuel > > > sessionInfo() > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > drosgenome1 drosgenome1cdf annotate annaffy KEGG > "1.10.0" "1.10.0" "1.8.0" "1.2.0" "1.8.1" > GO affy Biobase > "1.8.2" "1.8.1" "1.8.0" > > > ===================================== > drosgenome1 INSTALL INFO > > > biocLite("drosgenome1") > > Running bioCLite version 0.1 with R version 2.2.1 > > Running biocinstall version 1.1 with R version 2.2.1 > trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7 /src/contrib/drosgenome1_1.10.0.tar.gz' > Content type 'application/x-gzip' length 3374185 bytes > opened URL > ================================================== > downloaded 3295Kb > > * Installing *source* package 'drosgenome1' ... > ** R > ** data > ** moving datasets to lazyload DB > ** help > >>> Building/Updating help pages for package 'drosgenome1' > Formats: text html latex example > drosgenome1 text html latex > drosgenome1ACCNUM text html latex example > drosgenome1CHR text html latex example > drosgenome1CHRLOC text html latex example > drosgenome1ENZYME text html latex example > drosgenome1GENENAME text html latex example > drosgenome1GO text html latex example > drosgenome1GO2ALLPROBES text html latex example > drosgenome1GO2PROBE text html latex example > drosgenome1LOCUSID text html latex example > drosgenome1MAP text html latex example > drosgenome1ORGANISM text html latex example > drosgenome1PATH text html latex example > drosgenome1PMID text html latex example > drosgenome1PMID2PROBE text html latex example > drosgenome1QC text html latex > drosgenome1REFSEQ text html latex example > drosgenome1SUMFUNC text html latex example > drosgenome1SYMBOL text html latex example > drosgenome1UNIGENE text html latex example > ** building package indices ... > * DONE (drosgenome1) > > The downloaded packages are in > /tmp/RtmpU18540/downloaded_packages > > _______________________________________________ > 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 >

Emmanuel Levy wrote: > Dear Bioconductor community, > > I just started working with the drosgenome1 environment. > When I try to get the gene names from drosgenome1GENENAME, > I only get 5 gene names and 14005 NA values. > > >>table(GN) > > GN > Fas (TNF receptor superfamily member) > 1 > FBJ murine osteosarcoma viral oncogene homolog > 1 > interleukin 10 > 1 > interleukin 2 > 1 > interleukin 4 > 1 > NA > 14005 > > A couple of other environments seem to be empty (SUMFUNC, PATH ...) > > Is that normal? I don't know about normal, but it is correct: > drosgenome1() Quality control information for drosgenome1 Date built: Created: Wed Jan 4 18:17:19 2006 Number of probes: 14010 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: drosgenome1ACCNUM found 14010 of 14010 drosgenome1CHRLOC found 13244 of 14010 drosgenome1CHR found 13252 of 14010 drosgenome1ENZYME found 0 of 14010 drosgenome1GENENAME found 5 of 14010 <===== only 5 names drosgenome1GO found 8749 of 14010 drosgenome1LOCUSID found 13252 of 14010 drosgenome1MAP found 13233 of 14010 drosgenome1PATH found 0 of 14010 drosgenome1PMID found 13252 of 14010 drosgenome1REFSEQ found 13249 of 14010 drosgenome1SUMFUNC found 0 of 14010 drosgenome1SYMBOL found 13252 of 14010 drosgenome1UNIGENE found 13129 of 14010 Mappings found for non-probe based rda files: drosgenome1GO2ALLPROBES found 5586 drosgenome1GO2PROBE found 4063 drosgenome1ORGANISM found 1 drosgenome1PMID2PROBE found 9353 I don't know why there aren't more names, considering most of the really cool gene names come from the fly guys (frizzled, sonic hedgehog, son of sevenless, etc). Maybe Ting knows why there are so few names? Best, Jim > > Many thanks in advance for your comments, > > Emmanuel > > >>sessionInfo() > > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > drosgenome1 drosgenome1cdf annotate annaffy KEGG > "1.10.0" "1.10.0" "1.8.0" "1.2.0" "1.8.1" > GO affy Biobase > "1.8.2" "1.8.1" "1.8.0" > > > ===================================== > drosgenome1 INSTALL INFO > > >>biocLite("drosgenome1") > > > Running bioCLite version 0.1 with R version 2.2.1 > > Running biocinstall version 1.1 with R version 2.2.1 > trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7 /src/contrib/drosgenome1_1.10.0.tar.gz' > Content type 'application/x-gzip' length 3374185 bytes > opened URL > ================================================== > downloaded 3295Kb > > * Installing *source* package 'drosgenome1' ... > ** R > ** data > ** moving datasets to lazyload DB > ** help > >>> Building/Updating help pages for package 'drosgenome1' > Formats: text html latex example > drosgenome1 text html latex > drosgenome1ACCNUM text html latex example > drosgenome1CHR text html latex example > drosgenome1CHRLOC text html latex example > drosgenome1ENZYME text html latex example > drosgenome1GENENAME text html latex example > drosgenome1GO text html latex example > drosgenome1GO2ALLPROBES text html latex example > drosgenome1GO2PROBE text html latex example > drosgenome1LOCUSID text html latex example > drosgenome1MAP text html latex example > drosgenome1ORGANISM text html latex example > drosgenome1PATH text html latex example > drosgenome1PMID text html latex example > drosgenome1PMID2PROBE text html latex example > drosgenome1QC text html latex > drosgenome1REFSEQ text html latex example > drosgenome1SUMFUNC text html latex example > drosgenome1SYMBOL text html latex example > drosgenome1UNIGENE text html latex example > ** building package indices ... > * DONE (drosgenome1) > > The downloaded packages are in > /tmp/RtmpU18540/downloaded_packages > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi Emmanuel, I just notice that even thought there are only 5 gene names in this package, there are still 13252 SYMBOLs: drosgenome1SYMBOL found 13252 of 14010 I believe they are as useful as GENENAMEs: > head(as.list(drosgenome1SYMBOL)) $`155157_at` [1] "CycG" $`155122_at` [1] "CG9411" $`155036_at` [1] "CG1416" $`154985_at` [1] "CG9083" $`154948_at` [1] "eIF2B-epsilon" $`154899_at` [1] "lid" It seems that NCBI only provide the gene symbols for these probes in the downloadable files. I don't think we can do anything on this unless NCBI provides them. HTH, Ting ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Thu, 23 Mar 2006, Emmanuel Levy wrote: > Dear Bioconductor community, > > I just started working with the drosgenome1 environment. > When I try to get the gene names from drosgenome1GENENAME, > I only get 5 gene names and 14005 NA values. > > > table(GN) > GN > Fas (TNF receptor superfamily member) > 1 > FBJ murine osteosarcoma viral oncogene homolog > 1 > interleukin 10 > 1 > interleukin 2 > 1 > interleukin 4 > 1 > NA > 14005 > > A couple of other environments seem to be empty (SUMFUNC, PATH ...) > > Is that normal? > > Many thanks in advance for your comments, > > Emmanuel > > > sessionInfo() > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > drosgenome1 drosgenome1cdf annotate annaffy KEGG > "1.10.0" "1.10.0" "1.8.0" "1.2.0" "1.8.1" > GO affy Biobase > "1.8.2" "1.8.1" "1.8.0" > > > ===================================== > drosgenome1 INSTALL INFO > > > biocLite("drosgenome1") > > Running bioCLite version 0.1 with R version 2.2.1 > > Running biocinstall version 1.1 with R version 2.2.1 > trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7 /src/contrib/drosgenome1_1.10.0.tar.gz' > Content type 'application/x-gzip' length 3374185 bytes > opened URL > ================================================== > downloaded 3295Kb > > * Installing *source* package 'drosgenome1' ... > ** R > ** data > ** moving datasets to lazyload DB > ** help > >>> Building/Updating help pages for package 'drosgenome1' > Formats: text html latex example > drosgenome1 text html latex > drosgenome1ACCNUM text html latex example > drosgenome1CHR text html latex example > drosgenome1CHRLOC text html latex example > drosgenome1ENZYME text html latex example > drosgenome1GENENAME text html latex example > drosgenome1GO text html latex example > drosgenome1GO2ALLPROBES text html latex example > drosgenome1GO2PROBE text html latex example > drosgenome1LOCUSID text html latex example > drosgenome1MAP text html latex example > drosgenome1ORGANISM text html latex example > drosgenome1PATH text html latex example > drosgenome1PMID text html latex example > drosgenome1PMID2PROBE text html latex example > drosgenome1QC text html latex > drosgenome1REFSEQ text html latex example > drosgenome1SUMFUNC text html latex example > drosgenome1SYMBOL text html latex example > drosgenome1UNIGENE text html latex example > ** building package indices ... > * DONE (drosgenome1) > > The downloaded packages are in > /tmp/RtmpU18540/downloaded_packages > > _______________________________________________ > 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 >