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

Abhishek Pratap abhishek.vit at gmail.com
Wed Jun 25 01:32:27 CEST 2014

just for completeness I found the following work from Aron et al to be
useful. They have looked the the probeset specificity, coverage etc to
select an optimal probeset for a gene thereby enabling simple one to
one mapping.

Jetset: selecting an optimal microarray probe set to represent a gene
Qiyuan Li, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi, and
Aron C. Eklund
BMC Bioinformatics 2011, 12:474



On Mon, Jun 23, 2014 at 11:56 AM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> Thanks everyone specially for replying on the weekend.
> Cheers!
> -Abhi
> 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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