[BioC] converting probeset id to gene id's : fRMA

Abhishek Pratap abhishek.vit at gmail.com
Mon Jun 23 20:56:55 CEST 2014

Thanks everyone specially for replying on the weekend.


On Mon, Jun 23, 2014 at 10:18 AM, Federico Lasa <felasa at gmail.com> wrote:
> Another thing to consider is the platform you are using, it might be
> relevant since some Affy chips (i.e. HuGene 1.0 ST) can be summarized
> in different ways (probeset or core if i recall correctly).
> On Sun, Jun 22, 2014 at 11:14 PM, Peter Langfelder
> <peter.langfelder at gmail.com> wrote:
>> On Fri, Jun 20, 2014 at 5:05 PM, Abhishek Pratap <abhishek.vit at gmail.com> wrote:
>>> Hey Guys
>>> I am using fRMA to normalize n summarize some affy data. Post
>>> normalization I am getting 54k uniq probe id's in the eSet.
>>> I am wondering whats the best way to convert this expressionSet into a
>>> gene level data. I thought fRMA's documentation said it would produce
>>> gene level summarized values but I dont see that in the result. Can
>>> fRMA do that or is there any other standard way of achieving this in
>>> BioC.
>> One way to get from probe-level data to gene-level data is the
>> function collapseRows from the CRAN package WGCNA. The approach is
>> described in
>> Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR,
>> Horvath S (2011) Strategies for aggregating gene expression data: The
>> collapseRows R function. BMC Bioinformatics12:322,
>> http://www.biomedcentral.com/1471-2105/12/322
>> and some more information, including an example, is provided at
>> http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/collapseRows/
>> You do need to supply the probe to gene mapping, which is available
>> either from the chip manufacturer (presumably Affymetrix) or in an
>> appropriate Bioconductor package.
>> HTH,
>> Peter
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