Marc? A little problem. When I modernize old gene symbols, some of them are not exited. e.g. select(org.Hs.eg.db, keys = c("9-Mar","5_8S_rRNA","384D8-2"), cols="SYMBOL", keytype="ALIAS")$SYMBOL Error in .select(x, keys, cols, keytype, jointype = jointype) : keys must be of the same keytype as the actual keytype For these old gene symbols, I want to return the same. The output I hope are as follow. Because I have a long list. ALIAS SYMBOL 9-Mar 9-Mar 5_8S_rRNA 5_8S_rRNA 384D8-2 384D8-2 On Fri, Mar 15, 2013 at 11:00 PM, Jinyan Huang <jhuang at="" hsph.harvard.edu=""> wrote: > Marc? > > Thank you very much for you help. You reply really make sense to me. I > have a list of old gene symbols that I simply want to modernize. You > code is what I want. > > On Fri, Mar 15, 2013 at 8:32 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> Hi Jinyan, >> >> It depends. It depends on what you are using for annotations, and also >> which version of bioconductor/R you are using. If you are using packages >> from the release last fall for example, then those things will have been >> updated back then. We are currently in the middle of updating these things >> right now for the upcoming spring release. And if you are using a web >> service like biomaRt, things may have already been updated very recently. >> So it depends on what you are using for annotations... >> >> Unless maybe you are actually asking about what to do with a list of old >> gene symbols that you simply want to modernize. In that case, I think you >> want do do something like this: >> >> library(org.Hs.eg.db) >> select(org.Hs.eg.db, keys = c("CRSP6","KIAA0804"), cols="SYMBOL", >> keytype="ALIAS") >> >> Hope this helps, >> >> >> Marc >> >> >> >> On 03/14/2013 10:09 PM, Jinyan Huang wrote: >>> >>> Dear expert, >>> >>> Is there some bioconductor package to update Gene symbol ? >>> >>> e.g. >>> CRSP6 update to MED17. >>> http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/gene/9440 >>> >>> KIAA0804 update to VPS8 >>> http://www.ncbi.nlm.nih.gov.ezp- prod1.hul.harvard.edu/gene/?term=KIAA0804 >>> >>> -- >>> Best wishes, >>> >>> Jinyan HUANG >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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 > > > > -- > Best wishes, > > Jinyan HUANG -- Best wishes, Jinyan HUANG