I am working on the Infinium® CoreExome-24 v1.2 BeadChip data that I want to develop an automated workflow for, and there doesn't appear to be an annotation set for this chip. Are we able to provide our own annotation set? If so, are there specific files from the Illumina chip support files? Is there a format guide for the annotation?

Thank you in advance for your help.

Justin

Hi,

Yes, you can provide your own annotation package for this chip. I'm not familiar with these data but with some help from a colleague (thanks Jim!) it sounds like they're similar to the infinium chip packages

https://www.bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg19.html

or the methylation chip packages

https://www.bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html

To see a full list, go to the biocViews page ad type 'methylation' in the top right search box:

https://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData

You may need to create one package for processing the array data and another for annotating it with the closest genes. Kasper has provided a script for creating the data objects in the IlluminaHumanMethylationEPICanno.* packages in scripts/manifest.R. I would encourage you to contact Kasper or Tim for more guidance in putting a package together.

Valerie