[BioC] Specific annotation information from ExpressionSet

Daniel Brewer daniel.brewer at icr.ac.uk
Thu May 22 11:06:12 CEST 2008

No you are not missing anything.  I thought this was a useful feature
and so probably some one had done it before and submitted it to
bioconductor, that is normally the case.  I will just have to code it


Sean Davis wrote:
> On Wed, May 21, 2008 at 7:47 AM, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
>> Hello,
>> Is there any functions in bioconductor that can take an ExpressionSet,
>> find the correct annotation object and then get information? So the
>> function would use annotation() to get the object and then use that
>> object for a specific purpose
>> I have two uses for this:
>> 1) Given a REFSEQ ID find the corresponding probes in an ExpressionSet
>> and print the expression for those probes e.g.
>> getExprFromREFSEQ(REFSEQID, ExpressionSet)
>> 2) Given a probe and ExpressionSet find the gene symbol.
>> getSymbol(ExpressionSet, ProbeID)
>> If not, any ideas on the best way to do this?
> There are not functions for this, I do not think.  However, you could,
> in a pretty straightforward way, write a function to extract the
> annotation slot (when it has something in it--it is not guaranteed to
> be non-NULL), load the appropriate annotation package if it exists,
> and then do the lookups you want.  Or is there some other detail that
> I am missing from your post?
> Sean

Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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