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

Bernd Klaus bernd.klaus at embl.de
Sun Jun 22 16:21:32 CEST 2014

Hi Abhi,

I am not familiar with the fRMA package but the 
ExpressioSet you have have after normalization should
contain probset ids of some sort in the featureData 
slot, try


These id can then be easily mapped to e.g.  ENSEMBL IDs using
an appropriate chip-annotation database, see


for an example, which uses  the Human Genome U133 2.0 chip.
However similar databases are available for many
microarrays on Bioconductor.

Note that some probesets might map to multiple IDs.
The easiest thing is to discard them, however you can
of resolve these multiple mappings 
in a more sophisticated manner of course if you wish. 

Hope that helps,


On Fri, 20 Jun 2014 17:05:46 -0700
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.
> affyBatch_object <- ReadAffy(celfile.path=data_dir))
> normData1 <- frma(affyBatch_object, summarize="random_effect")
> appreciate any pointers.
> Thanks!
> -Abhi
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