Illumina annotation problem - illuminaHumanv2GENENAME

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McClellan, Elizabeth Ann ▴ 20

@mcclellan-elizabeth-ann-3192

Last seen 10.2 years ago

Dear Users, I have summarized data from an Illumina Human-6 v2 array with IDs numbered "10008", "10010",,...,"7650767", "7650768", and I am trying to look at functions of or get some information about some of these genes. I am using the illuminaHumanv2.db package and get a "NULL" output for any function that is supposed to take my probeset name as input, e.g. illuminaHumanv2GO[["10008"]] or illuminaHumanv2SYMBOL[["10008"]]. I have noticed that Illumina IDs such as "ILMN_1001" work properly with these functions, but I don't have such a prefix. I still get nothing if I strip off the "ILMN_". I visited Illumina's "Annotation Files Archive" with no avail. Is there a way to get gene names, symbols, anything, with these types of IDs? Here is my relevant session info: R version 2.8.0 (2008-10-20) other attached packages: [1] GOstats_2.8.0 Category_2.8.1 [3] genefilter_1.22.0 survival_2.34-1 [5] RBGL_1.18.0 annotate_1.20.1 [7] xtable_1.5-3 graph_1.20.0 [9] GO.db_2.2.5 illuminaHumanv2.db_1.1.3 [11] RSQLite_0.7-1 DBI_0.2-4 [13] AnnotationDbi_1.4.1 Biobase_2.2.1 Thank you, Elizabeth Elizabeth McClellan Department of Statistical Science Southern Methodist University

GO illuminaHumanv2 GO illuminaHumanv2 • 1.1k views

ADD COMMENT • link updated 15.9 years ago by Lynn Amon ▴ 280 • written 15.9 years ago by McClellan, Elizabeth Ann ▴ 20

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Lynn Amon ▴ 280

@lynn-amon-2429

Last seen 10.2 years ago

Use illuminaHumanv2BeadID.db instead. You might want to take the one from the devel version instead of the release version as there were some problems with the initial package. Lynn McClellan, Elizabeth Ann wrote: > Dear Users, > > I have summarized data from an Illumina Human-6 v2 array with IDs numbered "10008", "10010",,...,"7650767", "7650768", and I am trying to look at functions of or get some information about some of these genes. I am using the illuminaHumanv2.db package and get a "NULL" output for any function that is supposed to take my probeset name as input, e.g. illuminaHumanv2GO[["10008"]] or illuminaHumanv2SYMBOL[["10008"]]. I have noticed that Illumina IDs such as "ILMN_1001" work properly with these functions, but I don't have such a prefix. I still get nothing if I strip off the "ILMN_". I visited Illumina's "Annotation Files Archive" with no avail. Is there a way to get gene names, symbols, anything, with these types of IDs? > > Here is my relevant session info: > > R version 2.8.0 (2008-10-20) > other attached packages: > [1] GOstats_2.8.0 Category_2.8.1 > [3] genefilter_1.22.0 survival_2.34-1 > [5] RBGL_1.18.0 annotate_1.20.1 > [7] xtable_1.5-3 graph_1.20.0 > [9] GO.db_2.2.5 illuminaHumanv2.db_1.1.3 > [11] RSQLite_0.7-1 DBI_0.2-4 > [13] AnnotationDbi_1.4.1 Biobase_2.2.1 > > Thank you, > Elizabeth > > > Elizabeth McClellan > Department of Statistical Science > Southern Methodist University > > _______________________________________________ > 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 • link 15.9 years ago Lynn Amon ▴ 280

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Thank you! Problem solved. Elizabeth McClellan Department of Statistical Science Southern Methodist University ________________________________________ From: Lynn Amon [lamon@fhcrc.org] Sent: Monday, December 15, 2008 4:28 PM To: McClellan, Elizabeth Ann Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Illumina annotation problem - illuminaHumanv2GENENAME Use illuminaHumanv2BeadID.db instead. You might want to take the one from the devel version instead of the release version as there were some problems with the initial package. Lynn McClellan, Elizabeth Ann wrote: > Dear Users, > > I have summarized data from an Illumina Human-6 v2 array with IDs numbered "10008", "10010",,...,"7650767", "7650768", and I am trying to look at functions of or get some information about some of these genes. I am using the illuminaHumanv2.db package and get a "NULL" output for any function that is supposed to take my probeset name as input, e.g. illuminaHumanv2GO[["10008"]] or illuminaHumanv2SYMBOL[["10008"]]. I have noticed that Illumina IDs such as "ILMN_1001" work properly with these functions, but I don't have such a prefix. I still get nothing if I strip off the "ILMN_". I visited Illumina's "Annotation Files Archive" with no avail. Is there a way to get gene names, symbols, anything, with these types of IDs? > > Here is my relevant session info: > > R version 2.8.0 (2008-10-20) > other attached packages: > [1] GOstats_2.8.0 Category_2.8.1 > [3] genefilter_1.22.0 survival_2.34-1 > [5] RBGL_1.18.0 annotate_1.20.1 > [7] xtable_1.5-3 graph_1.20.0 > [9] GO.db_2.2.5 illuminaHumanv2.db_1.1.3 > [11] RSQLite_0.7-1 DBI_0.2-4 > [13] AnnotationDbi_1.4.1 Biobase_2.2.1 > > Thank you, > Elizabeth > > > Elizabeth McClellan > Department of Statistical Science > Southern Methodist University > > _______________________________________________ > 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 • link 15.9 years ago McClellan, Elizabeth Ann ▴ 20

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