On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie@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.

Timothy




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