On Thu, Oct 28, 2010 at 7:44 AM, Timothy Wu <2huggie@gmail.com> wrote:

> 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.
>
>
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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