quick question, are there any arrays like this on GEO, and if so, can you
just use the GPL description file to map the features?

I have been writing coercions from ExpressionSets of various array types
(mostly hgu133av2 and hgu133plus2, to be honest) to SummarizedExperiments,
which make the process a lot easier.  In fact, oftentimes you can get a
reasonably useful mapping by using the GEOquery package for similar arrays
and coercing the genomic coordinates to a GenomicRanges, whereupon the vast
amount of UCSC, biomaRt, and GenomicFeatures data is immediately available
to you.

So getting back to your question, I did a quick Google search, and sure
enough, in the biomaRt user's guide, there are mappings for probes from
this array.  It's not necessarily as streamlined as a .db package, but from
personal experience, those are not always frustration-free either.  Take a
look at page 20 of this PDF:

http://www.bioconductor.org/packages/2.11/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf

Hope this helps.  My recent experience is that mapping everything to
genomic coordinates makes it easier to compare across platforms (though
still not "easy").




On Sat, Sep 1, 2012 at 3:21 AM, Constanze Schmitt [guest] <
guest@bioconductor.org> wrote:

>
> Dear All,
>
> i'm using Bioconductor and R for gene expression analysis and i have a
> short question: which Bioconductor chip type/annotation package
> corresponds to the Agilent Chip G4858A-039494 (SurePrint G3 Human Gene
> Expression 8x60K v2 Microarray)? I haven't got the data yet and i haven't
> managed to find a matching "hgug..." ID. It would be great if someone could
> help.
>
>
> Best wishes,
>
> Constanze
>
>  -- output of sessionInfo():
>
> I haven't used any code yet as i still don't have the data (-; .
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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