Jinyan Huang | 16 Mar 06:58 2013
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Re: Gene symbol update.

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
>>>
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>>
>>
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>
>
>
> --
> Best wishes,
>
> Jinyan HUANG

--
Best wishes,

Jinyan HUANG

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