[BioC] Filtering in Beadarray package

[Sean Davis]

On Wed, May 28, 2008 at 9:42 PM, ss <affysnp at gmail.com> wrote:
> Thanks Mark for the suggestions and references. I will check them out.
> A question which is slightly different from this thread that I noticed in
> the vignette of Beadarray that gene name information could be retrieved
> by using:
>
>>genename=mget(ids, illuminaHumanv1GENENAME, ifnotfound=NA)
>
> I wonder whether gene description or definition information could also
> be retrieved using the similar way like mget() or other commands by
> any chance?

If you type:

help(package=illuminaHumanv1)

You can see the various mappings available.

The command:

illuminaHumanv1()

will give you some summary information.

You can read the vignettes in the annotate package for more
information.  The examples there do not use the illumina annotation
package, but you will hopefully get the idea.

Sean


> On Wed, May 28, 2008 at 6:13 AM, Mark Dunning <md392 at cam.ac.uk> wrote:
>
>> Hi Allen,
>> For filtering Illumina data, most people seem to use the 'detection pval'
>> column and remove genes which are not present on *any* array in the
>> experiment. However, I agree with Sean's comment that a gene being expressed
>> all the time is not enough to qualify it as being "interesting" and
>> filtering based on variability might be more appropriate.
>>
>> I would also use the data that have not been background adjusted by
>> BeadStudio. The background adjustment that they use in BaedStudio creates a
>> lot of negative values which are difficult to deal with if you use the
>> standard log2 transformation for microarray data. The way around this for
>> Illumina data is to use the VST transformation in the lumi package (or avoid
>> the problem altogether by not background adjusting....)
>>
>>
>> You might like to check out the following references for details on
>> processing Illumina data ;)
>>
>> -Lin et al. Model-based variance-stabilizing transformation for Illumina
>> microarray data, NAR, (2008)
>>
>> -Dunning et al. Statistical issues in the analysis of Illumina data, BMC
>> Bioinformatics, (2008)
>>
>> Regards,
>>
>> Mark
>>
>>
>> On 28 May 2008, at 00:51, ss 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'.
>>
>> 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 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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>>
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>>
>
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