[BioC] annotation of affymetrix microarray data

[Wolfgang Huber]

Dear Katie

from the way you phrase your question I presume you have not yet had the 
chance to familiarise yourself with the basics of R programming?

If so, doing that would be a good starting point. It's worth the effort. 
Without, you will not have much fun with Bioconductor. With a basic 
knowledge of R, I am sure the examples in the vignettes (and in fact, 
many other things in life) will start making more sense to you, and, 
importantly, you will be able to modify the workflows explained in the 
vignettes to match exactly your needs.

	Best wishes
	Wolfgang


Taylor, Katie ha scritto:
> Dear Sir/Madam,
> 
> I hope that this email finds you well. I am currently undertaking a PhD and I have performed some arrays on the illumina platforms. I have also downloaded some affymetrix data from GEO (GDS2609) which I have successfully analysed in bioconductor. I am new to bioconductor however and so I rely heavily on the worked examples given in the pdf documentation at bioconductor. I recently tried to use the annaffy package to annotate the data but I was unsuccessful. I have tried to use the script that is given as an example in the annaffy pdf but it won't work on my data set. I am sure that it is probably something that I am doing wrong. Instead of entering 
> 
>> data(aafExpr)
> 
> I entered:
> 
>> data(GDS2609)
> 
> as this is the name of the file that I want to open. I can get individual symbols but not a list or table. I tried emailing the person who wrote the annaffy pdf but he advised me to email the bioconductor emailing list - I hope I am emailing the correct place. If you could give me any advice I would be really grateful. I am trying to annotate the GDS2609 dataset and I'm hoping that you will be able to help me. I appreciate any help that you can offer me. 
> 
> Thank you and best wishes, 
> 
> Katie
> 
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-- 


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