Thanks Sean! I always get your help!
Could you recommend the filtering criteria for normalized Illumina data?
I figured I maybe can use 'detection pval' to deal with this task. My
colleague
told me that a probe could be removed from further analysis if the
'detection
pval' is greater than 0.05 because it could be regarded as 'non present'.

Another question is that I got three data files from the microarray facility
and I wonder which one I should get started. One is the raw data file,
the second one is the raw data after background subtraction and, the
third one is called rSef (normalized in Illumina Beadarray studio). I guess
I may go with the first one (without background adjustment). If you can
shed some light, that will be wonderful.

I will check out 'genefilter' package.

Have a good evening!

Allen

On Tue, May 27, 2008 at 7:10 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Tue, May 27, 2008 at 6:30 PM, ss <affysnp@gmail.com> wrote:
> > Hi all,
> >
> > I am wondering whether filtering function is available in Beadarray
> package.
> >
> > Thank you very much!
>
> Hi, Allen.  The nice thing about Bioconductor is that you do not need
> to restrict yourself to the functionality of a single package.  Many
> of the packages work well together.  You might want to take a look at
> the genefilter package.  Beadarray has a data structure similar to the
> ExpressionSet used in the genefilter vignette.  If you have questions
> after working through those examples, please feel free to write back
> with what you tried and how it didn't work.
>
> Sean
>

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