Sean,

Thanks for the heads-up. I will read through those documents.

Have a great weekend!

Allen

On Fri, May 23, 2008 at 8:03 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Thu, May 22, 2008 at 7:05 PM, ss <affysnp@gmail.com> wrote:
> > Hi Sean,
> >
> > Thanks for pointing it out. The reason that I would like to supply with a
> > txt
> > file of Illumina gene expression data is that I find it hard to use
> either
> > beadarray
> > or lumi to subset gene expression data based on genes of your interest.
> > Please
> > correct me if I am wrong. Anyway, I will check it out.
>
> I do not find it particularly difficult to subset genes and samples in
> either of those packages, and one can always use the exprs() method
> for each to extract a raw matrix and subset that.  For the beadarray
> package, see the vignette entitled "beadsummary.pdf", paying
> particular attention to the "BSData" section.  Similar methods work
> with the lumi package.
>
> If by "find it hard to use either beadarray or lumi to subset..." you
> mean that you do not know where to start, I have given a hint above.
> Also, many of the data classes used in Bioconductor are based on the
> ExpressionSet class (or the eSet class).  There is extensive
> documentation in the Biobase package for taking subsets of data that
> will likely apply to both beadarray and lumi subsetting.  It is
> worthwhile working through the examples in the various vignettes and
> reading help pages if you would like to maximize your productivity
> with bioconductor.
>
> Hope that helps get you going.
>
> Sean
>
> > On Thu, May 22, 2008 at 4:29 PM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
> >>
> >> Hi, Allen.  As for illumina data, I would look into using the
> >> beadarray or lumi packages.  No reason to use excel for these types of
> >> things.
> >>
> >> As for heatmap, try searching the mailing list here:
> >>
> >> http://dir.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> If you type in the keywords heatmap and color, you will see numerous
> >> potential possibilities.
> >>
> >> Sean
> >
> >
>

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