[BioC] annotation of affymetrix microarray data

[Loren Engrav]

Absolutely true
And the manual by Dr. Girke at
<http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual>
 is very helpful for novices (me)


> From: Wolfgang Huber <whuber at embl.de>
> Date: Tue, 27 Apr 2010 20:58:22 +0200
> To: "Taylor, Katie" <kt70 at leicester.ac.uk>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] annotation of affymetrix microarray data
> 
> 
> 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
> 
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