Question

Is There A R Package For The Annotation Of Help Assay?

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11.8 years ago

jlshi.nudt ▴ 240

I am studying some methylation data generated by HELP assay. Its IDs are MSPI0406S00000183, MSPI0406S00000238, MSPI0406S00000239

Where can I find the annotations for these IDS? Thank you.

methylation annotation • 2.3k views

ADD COMMENT • link updated 11.8 years ago by Sean Davis 27k • written 11.8 years ago by jlshi.nudt ▴ 240

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Hi, I am facing the same problem as you faced around 2 years ago. I wish to convert a very long list of HELP assay probe IDs into their respective gene symbols and could not find a way after searching and trying different tools for long. The only way that I found is to google search them one by one - very exhaustive as the list is really long. Is there any online tool available that I can simply upload the probe ID list and get the converted gene list (like those of DAVID)? Thanks.

ADD REPLY • link 10.0 years ago by libralsk • 0

score 2 · Answer 1 · 2013-03-02

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11.8 years ago

Sean Davis 27k

It is unusual to have array data without getting the annotation associated with it, so you might go back to the array data source. However, it does look like this platform is available via NCBI GEO.

library(GEOquery)
gpl = getGEO('GPL6604')

ADD COMMENT • link 11.8 years ago by Sean Davis 27k

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Thank you. Is there any R package like "hgu133a.db" which can be used directly?

ADD REPLY • link 11.8 years ago by jlshi.nudt ▴ 240

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Not that I know of. This is not a gene-based array, so gene-based annotation packages don't make much sense in this case.

ADD REPLY • link 11.8 years ago by Sean Davis 27k