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

[Peter Langfelder]

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