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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

From another thread I now know that this is just a regular microarray. So based on that, I think you will find what you need for this here: http://www.bioconductor.org/packages/2.10/bioc/vignettes/AnnotationDbi /inst/doc/SQLForge.pdf Marc On 09/01/2012 03:21 AM, Constanze Schmitt [guest] 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor