[BioC] Getting annotation into eset

[Marc Carlson]

Hi Timothy,

It sounds like you might just be asking how to set the annotation slot
on the ExpressionSet object?  You have not given us a lot of
information, so it is hard to know.  But if that is the case, then you
might also try:

library(Biobase)
openVignette()

Or just go here:

http://www.bioconductor.org/help/bioc-views/release/bioc/html/Biobase.html

Or look at the manual page for ExpressionSets:

?ExpressionSet

And learn about the annotation() accessor method that is defined for these.


  Marc




On 10/28/2010 04:48 AM, Sean Davis wrote:
> On Thu, Oct 28, 2010 at 7:44 AM, Timothy Wu <2huggie at gmail.com> wrote:
>
>   
>> On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>>     
>>>
>>> On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie at gmail.com> wrote:
>>>
>>>       
>>>> Hi,
>>>>
>>>> I noticed that when I obtain eset from GEO matrix file via GEOquery, the
>>>> result obtained from limma analysis includes the annotation information.
>>>> However, eset obtained from CEL files via ReadAffy() and GCRMA
>>>>         
>> threestep()
>>     
>>>> do not include those annotations. How do I infuse the annotations into
>>>> eset
>>>> (preferred) before limma analysis? Or maybe during limma result if that
>>>>         
>> is
>>     
>>>> more proper. The platform is U133 plus 2.
>>>>
>>>> Any help appreciated, thank in advance.
>>>>
>>>>
>>>>         
>>> Hi, Timothy.  The easiest way to do this will depend on the details of
>>>       
>> the
>>     
>>> workflow you are using.  If you can provide those details, answering your
>>> question will be simpler.  To answer directly, though, you simply need to
>>> fill the featureData slot of the eSet with the annotation information.
>>>
>>> Sean
>>>
>>>       
>> Hi Sean,
>>
>> I am not sure what the workflow you're referring to.
>>
>> This is how I obtain the eset:
>>
>> ==
>> library(affy)
>> library(affyPLM)
>>
>> affybatch <- ReadAffy()
>> eset <<- threestep_gcrma(affybatch)
>> ==
>>
>> Are there package that I can use to fill the featureData? I am not very
>> skilled in R and what you says looks intimidating.
>>
>>
>>     
> Hi, Timothy.  You could look at the the AnnotationDbi package
> vignette: AnnotationDbi:
> How to use the ".db" annotation packages.  Also, you should look at the
> annotate bioconductor package.
>
> Sean
>
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>
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