[BioC] annotation of affymetrix microarray data

[Taylor, Katie]

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