Question: cram for new chips
1
gravatar for lack.justin
17 months ago by
lack.justin10
lack.justin10 wrote:

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

ADD COMMENTlink modified 16 months ago by Valerie Obenchain6.7k • written 17 months ago by lack.justin10

lack.justin were you able to create automated workflow? if so, could you please share the information on creating annotation and package?

ADD REPLYlink written 13 months ago by cpad01120
Answer: cram for new chips
0
gravatar for Valerie Obenchain
16 months ago by
United States
Valerie Obenchain6.7k wrote:

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

ADD COMMENTlink written 16 months ago by Valerie Obenchain6.7k

May be I am wrong here. But there is no manifest.R file either in  the source package  or post installation directory under scripts.  Manual mentions location of manifest.R as mentioned above.

Closest script name is: createAnno.R (probably).

Scripts are located here: IlluminaHumanMethylationEPICanno.ilm10b2.hg19/inst/scripts in source package and post installation here: .R/library/IlluminaHumanMethylationEPICanno.ilm10b2.hg19/scripts.

There is another script named "createAnno.Rout".

ADD REPLYlink modified 13 months ago • written 13 months ago by cpad01120
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