[BioC] Gene symbol update.
jhuang at hsph.harvard.edu
Sat Mar 16 06:58:52 CET 2013
A little problem. When I modernize old gene symbols, some of them are
select(org.Hs.eg.db, keys = c("9-Mar","5_8S_rRNA","384D8-2"),
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.
On Fri, Mar 15, 2013 at 11:00 PM, Jinyan Huang <jhuang at hsph.harvard.edu> wrote:
> 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:
>> select(org.Hs.eg.db, keys = c("CRSP6","KIAA0804"), cols="SYMBOL",
>> Hope this helps,
>> On 03/14/2013 10:09 PM, Jinyan Huang wrote:
>>> Dear expert,
>>> Is there some bioconductor package to update Gene symbol ?
>>> CRSP6 update to MED17.
>>> KIAA0804 update to VPS8
>>> Best wishes,
>>> Jinyan HUANG
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> Search the archives:
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> Search the archives:
> Best wishes,
> Jinyan HUANG
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