I want to thank you for the prompt answer. 

I know that the data from that URL has been preprocessed, it was just an example of custom Affymetrix. I found other
custom Affymetrix datasets that have raw data, that I need to preprocess (such as http://www.mdl.dk/Publications_sup7.htm). 
I also have the book that you mentioned, and the examples are on Affymetrix data and I can't use them on my dataset. I've tried 
but I get the same error - the object that I use must be an Affybatch.
I believe that are some special packages that can be used on custom data and I want to know which one.


Thank you again and I look forward to your answer,
Oana




________________________________
From: Wolfgang Huber <whuber@embl.de>

Cc: bioconductor@stat.math.ethz.ch
Sent: Tue, April 27, 2010 2:46:12 PM
Subject: Re: [BioC] custom Affymetrix


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
> 
> 
> 
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-- 

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


      
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