Question: Question about Illumina Infinium 450K
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gravatar for 99syzygy
8 months ago by
99syzygy0
99syzygy0 wrote:

Hi Bioinformaticians,

Could you possibly help me understand in simple terms what is a "probe" (ex: cg06928838 (GSTP1 gene)) in an Infinium HumanMethylation450K BeadChip and how is a probe "made"? I mean to get methylation values.

Am I correct in saying that probes target specific loci of genes, not the whole gene to get a methylation value?

I would appreciate all responses. Thanks!

ADD COMMENTlink modified 8 months ago by Charles Warden7.2k • written 8 months ago by 99syzygy0
1
gravatar for Charles Warden
8 months ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

You are correct: the 450k array provides methylation for CpG sites (or genotypes for some sites, and some methylation for individual sites that aren't in the CpG context).

You'll need to use some sort of method to define regions from your site signal (or at least have site annotations and your own way of looking for consistent signal among nearby sites).

ADD COMMENTlink written 8 months ago by Charles Warden7.2k
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