a question for Metadata package: hgu133a
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.3 years ago
Hi list, Please see the following: > package.version('hgu133a') [1] "1.12.0" > get('202990_at', hgu133aGENENAME) [1] "phosphorylase, glycogen" " liver (Hers disease, glycogen storage disease type VI)" > get('202100_at', hgu133aGENENAME) [1] "v-ral simian leukemia viral oncogene homolog B (ras related" [2] " GTP binding protein)" > get('202990_at', hgu133aGENENAME)[1] [1] "phosphorylase, glycogen" > get('202990_at', hgu133aGENENAME)[2] [1] " liver (Hers disease, glycogen storage disease type VI)" > get('202100_at', hgu133aGENENAME)[1] [1] "v-ral simian leukemia viral oncogene homolog B (ras related" > get('202100_at', hgu133aGENENAME)[2] [1] " GTP binding protein)" I understand that b/c there were ";" in the original annotations, the two parts were put into two separate fields. But does it make more sense just to combine them into one? It will make coding much easier. ...Tao
Leukemia Leukemia • 822 views
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@maria-stalteri-873
Last seen 8.1 years ago
Hi Tao, At least in the two examples you have given, it seems that the second field is just a continuation of the gene name, or description of the gene, so it would make more sense to combine the two fields, since they refer to the same gene. If a probeset maps to more than one gene, then it would make sense to have the different gene names in separate fields. Regards, Maria
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Shi, Tao <shidaxia at="" ...=""> writes: > > Hi list, > > Please see the following: > > > package.version('hgu133a') > [1] "1.12.0" > > get('202990_at', hgu133aGENENAME) > [1] "phosphorylase, glycogen" " liver (Hers disease, glycogen storage disease type VI)" > > get('202100_at', hgu133aGENENAME) > [1] "v-ral simian leukemia viral oncogene homolog B (ras related" > [2] " GTP binding protein)" > > > get('202990_at', hgu133aGENENAME)[1] > [1] "phosphorylase, glycogen" > > get('202990_at', hgu133aGENENAME)[2] > [1] " liver (Hers disease, glycogen storage disease type VI)" > > > get('202100_at', hgu133aGENENAME)[1] > [1] "v-ral simian leukemia viral oncogene homolog B (ras related" > > get('202100_at', hgu133aGENENAME)[2] > [1] " GTP binding protein)" > > I understand that b/c there were ";" in the original annotations, the two parts were put into two separate > fields. But does it make more sense just to combine them into one? It will make coding much easier. > > ...Tao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi, Tao, Thanks for the bug report. I will try to fix it next week. In package hgu133a, one probe set ID only maps to one Entrez Gene ID therefore should have only one gene name. So, a silly, temporary work around would be: x <- get('202100_at', hgu133aGENENAME) x <- paste(x, sep="", collapse="") Sorry for the inconvenience. If you also observe other problems in hgu133a, please let us know so that we can fix them all together. Many thanks. nianhua Nianhua Li Computational Biology, PHS, FHCRC
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