[BioC] link to KEGG

[Marc Carlson]

Hi Marcos,

I think that the most straightforward way to do this would be to use the
Annotation Packages.  You can read the vignette for AnnotationDbi to see
more here:

http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html


You didn't give me anything specific, so that makes it hard to answer
your question, but let's suppose that you are using the platform
hgu95av2 from Affy:

# 1st you would load the library for the corresponding annotation:
library(hgu95av2.db)
# then you would have some probes, lets call them yourProbes
yourProbes= c("1000_at",  "1001_at",  "1002_f_at")
# then you could look up the KEGG pathway IDs doing something like this:
mget(yourProbes, hgu95av2PATH, ifnotfound=NA)

hope this helps,


  Marc



Marcos Pinho wrote:
> Dear list,
>
> I have search extensively old postings but could not find an easy
> explanation on how to link my gene list generated after a diferential
> expression analysis with limma to a kegg pathway analysis. Any help would be
> greatly appreciated. Please keep in mind that I am a molecular biologist
> that can navigate through R , but it is always a challenge, therefore
> details and or examples are very helpful!
>
> cheers,
>
>   
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