[BioC] Filtering in Beadarray package

Sean Davis sdavis2 at mail.nih.gov
Wed May 28 02:14:56 CEST 2008

On Tue, May 27, 2008 at 7:51 PM, ss <affysnp at gmail.com> wrote:
> 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'.

You can do that, but make sure that you do not filter out the most
interesting genes (genes that are "on" in one condition and "off" in
another).  It might be better to filter based on something like
variance, as even highly-expressed genes that are unchanged across an
experiment are not useful for differential gene expression.  Again,
checking back through the list archives will turn up MANY discussions
on gene filtering.

> 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 would certainly look into the Illumina BeadStudio user guide for the
details of the various algorithms to make sure that you know what you
are choosing.  I agree that going with less-processed data is
generally better.

> I will check out 'genefilter' package.
> Have a good evening!
> Allen
> On Tue, May 27, 2008 at 7:10 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> On Tue, May 27, 2008 at 6:30 PM, ss <affysnp at 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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