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

[Abhishek Pratap]

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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor