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

Federico Lasa felasa at gmail.com
Mon Jun 23 19:18:28 CEST 2014

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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