R help - Apr 2013 - Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY

Hello All,

I need your help. I am analysing affymetrix data and have to select the
probe-set that has median expression among all the probe-sets for same
gene. This way I want to remove the redundancy by keeping the analysis
to single gene entry level. I am fully aware that it is not a nice thing
to do but I just have to do it.

To do so, I came across 'findLargest' function of 'genefilter'
package
but it's not well documented; and I do not know how to implement the
'findLargest' function. At this point I have:
esetRMA <- rma(mydata)

Could anybody guide me on how can I select single probeset with median
expression from multiple probe-sets corresponding to single gene and
discard others? Is there any other way to achieve so i.e. other than
using 'genefilter'?

Genefilter package:
http://www.bioconductor.org/packages/2.11/bioc/html/genefilter.html

Thanks

AK

-- 
Atul Kakrana
Delaware Technology Park

On 04/03/2013 03:17 PM, Atul Kakrana wrote:
> Hello All,
>
> I need your help. I am analysing affymetrix data and have to select the
> probe-set that has median expression among all the probe-sets for same
> gene. This way I want to remove the redundancy by keeping the analysis
> to single gene entry level. I am fully aware that it is not a nice thing
> to do but I just have to do it.
>
> To do so, I came across 'findLargest' function of
'genefilter' package
> but it's not well documented; and I do not know how to implement the
> 'findLargest' function. At this point I have:
> esetRMA <- rma(mydata)
>
> Could anybody guide me on how can I select single probeset with median
> expression from multiple probe-sets corresponding to single gene and
> discard others? Is there any other way to achieve so i.e. other than
> using 'genefilter'?
>
> Genefilter package:
> http://www.bioconductor.org/packages/2.11/bioc/html/genefilter.html
Hi Atul --It's a Bioconductor package, so might as well ask instead on the 
Bioconductor mailing list

   http://bioconductor.org/help/mailing-list/

As a reproducible example, load the "ALL" sample ExpressionSet,
Biobase and
genefilter packates

   library(Biobase)
   library(ALL)
   library(genefilter)

The three arguments to findLargest are the names of the probe sets

   featureNames(ALL)

the test statistic

   rowMedians(ALL)

and the chip from which the ExpressionSet is based

   annotation(ALL)

So the variable

   idx = findLargest(featureNames(ALL), rowMedians(ALL), annotation(ALL)

identifies the probes and

   ALL1 = ALL[idx,]

gets you the data you're interested in.

Again, follow-up questions should go to the Bioconductor mailing list.

Martin

>
> Thanks
>
> AK
>

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