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.

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