Question: Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
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gravatar for maden.sean
4.1 years ago by
maden.sean10
United States
maden.sean10 wrote:

From the 450k manifest data that I retrieve using getAnnotation() in minfi, how do I interpret variables UCSC_RefGene_Name and UCSC_RefGene_Group when there are several genes or groups listed (separated by a semicolon) for the same probe (that is, in the same row)?

Example:

For probe X, I have:

UCSC_RefGene_Name: Gene1;Gene2;Gene1

UCSC_RefGene_Group: TSS200;Body;1stExon

My guess for this probe would be that it maps to three distinct transcripts: 1. In TSS200 of first Gene1 transcript; 2. In Body of Gene2 transcript; 3. in 1stExon of second Gene1 transcript. Is this correct?

Best,

Sean

 

 

 

ADD COMMENTlink modified 4.1 years ago by Kasper Daniel Hansen6.4k • written 4.1 years ago by maden.sean10
Answer: Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
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gravatar for Kasper Daniel Hansen
4.1 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
This annotation is provided by Illumina and is unchanged. I don't use it myself, and have no comments on it. Best, Kasper On Fri, Oct 2, 2015 at 4:31 PM, maden.sean [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User maden.sean <https: support.bioconductor.org="" u="" 8348=""/> wrote Question: > Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names > <https: support.bioconductor.org="" p="" 72915=""/>: > > From the 450k manifest data that I retrieve using getAnnotation() in > minfi, how do I interpret variables UCSC_RefGene_Name and > UCSC_RefGene_Group when there are several genes or groups listed (separated > by a semicolon) for the same probe (that is, in the same row)? > > Example: > > For probe X, I have: > > UCSC_RefGene_Name: Gene1;Gene2;Gene1 > > UCSC_RefGene_Group: TSS200;Body;1stExon > > My guess for this probe would be that it maps to three distinct > transcripts: 1. In TSS200 of first Gene1 transcript; 2. In Body of Gene2 > transcript; 3. in 1stExon of second Gene1 transcript. Is this correct? > > Best, > > Sean > > > > > > > > ------------------------------ > > Post tags: illuminahumanmethylation450kanno.ilmn12.hg19, minfi, > illuminahumanmethylation450k.db, methylation > > You may reply via email or visit Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names >
ADD COMMENTlink written 4.1 years ago by Kasper Daniel Hansen6.4k
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