[BioC] custom Affymetrix

[Wolfgang Huber]

Dear Oana,

I am sure you have read the experiment description at the URL you kindly 
sent us, where it says "The final average log2 values are supplied as 
supplemental files to this GEO series." This indicates that the data 
producers consider no further background correction or normalize steps 
to be necessary.

For differential expresion, you might have a look, for instance, at the 
respective chapters in the book  http://www.bioconductor.org/pub/biocases
which discusses the other questions (differential analysis and 
clustering) you asked.

	Best wishes
	Wolfgang


Vermesan Oana scripsit 27/04/10 08:05:
> Good morning,
> 
> I started using Bioconductor about a month ago. I'm working with Affymetrix and Agilent data. I have the entire workflow
> and I know how to use the packages for this type of data. Recently I have found some custom Affymetrix data and I don't
> know how to process it. I have only an .xls file with the measured genes and a .txt with the clinical information. These two
> can be found here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5479. Can someone tell me which packages
> to use in order to do the background correction, to normalize the data and to do a differential analysis? I also need to do
> a hierarchical clustering. If someone could help me I would really appreciate that. 
> 
> Thank you,
> Oana
> 
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
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-- 


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