Question: a question for Metadata package: hgu133a
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gravatar for Shi, Tao
13.1 years ago by
Shi, Tao720
Shi, Tao720 wrote:
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 • 594 views
ADD COMMENTlink modified 13.1 years ago by Nianhua Li870 • written 13.1 years ago by Shi, Tao720
Answer: a question for Metadata package: hgu133a
0
gravatar for MARIA STALTERI
13.1 years ago by
MARIA STALTERI160 wrote:
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
ADD COMMENTlink written 13.1 years ago by MARIA STALTERI160
Answer: a question for Metadata package: hgu133a
0
gravatar for Nianhua Li
13.1 years ago by
Nianhua Li870
Nianhua Li870 wrote:
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
ADD COMMENTlink written 13.1 years ago by Nianhua Li870
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