[BioC] converting probe names to gene list

[Sean Davis]

Hi, Mark.  What chip are you using?  If you are using hgu133a, for example,
you can do:

 library(hgu133a)   # after installing the hgu133a package from bioC
metadata
 probeIDs <- ls(hgu133aSYMBOL)
 symbols <- mget(probeIDs,hgu133aSYMBOL)

You probably want to look at the annotate and annaffy packages to learn some
more detail.

Hope this gets you started.

Sean



On 3/21/06 12:24 PM, "mark salsburg" <mark.salsburg at gmail.com> wrote:

> I have a plain text file with 12,000 probe id names from an affymetrix chip.
> 
> Can someone please review the details of how to output out a plain text file
> with the GENE SYMBOLS
> 
> I am using AffyNet from Affymetrix.net and going to Batch Query in the
> Expression section where it says
> "Retrieve annotation for a probe list", where I search for "probe set id"
> and view the list with "gene list". Is this
> correct?
> 
> Some problems encountered so far:
> 
> 1) affynet tells me it can only export 3000 genes
> 2) afffynet changes the order of the outputted genes by putting probe ids
> that start with AFFY last. (they are in fact first)
> 2) affynet exports out more information than I need, I just need the gene
> symbol.
> 
> Can someone please lead me through the procedure to output out a simple text
> file of gene symbol?
> 
> thank you in advance
> 
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