[BioC] annotation of affymetrix microarray data

[Sean Davis]

On Tue, Apr 27, 2010 at 6:28 AM, Taylor, Katie <kt70 at leicester.ac.uk> wrote:
> 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.
>

Hi, Katie.  The data set is already annotated by NCBI GEO and
Affymetrix.  Try the following:

library(GEOquery)
gds <- GDS2eSet(getGEO('GDS2609'))
head(fData(gds))
varLabels(featureData(gds))

Also, it is worth noting that this GDS was run on the hgu133plus2
array, so you can also access the bioconductor annotation package that
matches, if you like.

Sean