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Question: annotations for arrays
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3.5 years ago by
Guest User12k
Guest User12k 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.
ADD COMMENTlink modified 3.5 years ago by Marc Carlson7.2k • written 3.5 years ago by Guest User12k
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gravatar for Marc Carlson
3.5 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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: http://www.bioconductor.org/packages/release/BiocViews.html#___ChipNam e 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 install.packages(). library('AnnotationForge') ?makeChipPackage ## 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, Marc 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. > > _______________________________________________ > 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
ADD COMMENTlink written 3.5 years ago by Marc Carlson7.2k
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