[BioC] annotations for arrays

Marc Carlson mcarlson at fhcrc.org
Mon Jun 9 18:56:17 CEST 2014

Hi Miki,

So the reason you can't find codes for these is that there are not 
packages made for these platforms yet. You can see all the existing 
packages listed here:


Anyhow what to do when there is not a package made already for your 
platform of interest? Just load up the AnnotationForge package and then 
call the new makeChipPackage() function. This package should allow you 
to make a chip package for anything that you have an organism package 
for (and if you need an org package there is a function that makes those 
too). Once you have made your package you can install it with 


## Then once you have called that function, you can install your package 
like this:
install.packages('<packageNameWithPath>', repos=NULL, type="source")

Let me know if you have any more questions,


On 06/06/2014 09:48 AM, Miki Blumenberg [guest] wrote:
> I am using VirtualArray and, while Affymetrix annotation files ID I could figure out,
> Such as: annotation(GSE26059) <- "hgu133a2".
> Where can I find the right codes for:
> Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381
> or ACG_SGF_CEA (GPL263) – noncommercial,
> RNG-MRC_HU25k_EVRY (GPL1496), – noncommercial,
> Wistar/Shiekhattar-human-44k-1.0 (GPL13402)
> Illumina HumanHT-12 V3.0 expression beadchip (GPL6947)
> Is there a way to include RNA_Seq data, e.g., GPL11154?
> Thanks,
>   Miki Blumenberg, NYU Med.School.
>   -- output of sessionInfo():
> --
> Sent via the guest posting facility at bioconductor.org.
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