[BioC] Summarizing two-channel data (RGList, MAList) for limma analysis

[Wolfgang Huber]

Dear Stephen

Hasn't the array vendor provided you already with some guidance on this?

If there are multiple probes with different sequences supposedly 
targeting the same gene, I think you need assess (in some automated way) 
the alignment of the probes to the genome and to the gene model in order 
to see which of them is the 'better' one.

	Best wishes
	Wolfgang



On 1/11/12 10:45 PM, Stephen Turner wrote:
> Hello.
>
> I have 4 Agilent two-channel arrays that I read in using read.maimages().
> I've done normalization and background subtraction. How do I now summarize
> the probe information (62976 probes) to gene-level expression values (39430
> entrez RNAs, 16251 lincRNAs). I normally did this using rma() or gcrma()
> from the affy package when I have Affymetrix data.
>
> Thanks,
>
> Stephen
>
> 	[[alternative HTML version deleted]]
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber