[BioC] Simple conceptual question

[Gustavo Fernández Bayón]

Hi everybody.  

Imagine I have my ideal, conceptual, pipeline for working with my Illumina 27k data:

A) Bead level intensities  

---> (color adjustment, background subtraction, normalization, …)

---> B) Meth and Unmeth intensities

---> (get ratios)

----> C) Beta values or M-values

As I understand, proper normalization, if needed, should be done over the Red and Green signals (bead level signals, I know there are two types of beads, M and U, for each locus, and that each locus is assigned to a fixed color channel. I have studied the code in the minfi package, although it is for 450k, just to understand how these values get converted).  

Q1) Am I right? Or, is there any way we can normalize by using the M and U signals?  

Q2) As an example, I have downloaded raw data from a given GEO dataset, and found only the M and U (Signal A and B, in their nomenclature) data. At that, point, I think I cannot do neither normalization nor QC, can I? What happens if somebody tries to normalize these signals and, for example, color balance was not adjusted? Or does GenomeStudio care about that?

Q3) People from another lab want us to take a look to some methylation datasets they have, and I am planning (having seen the facts above) to ask them for the .txt or .idat files, in order to do QC and normalization with lumi. Is that ok? Or is there any alternative? They claim they are having a lot of problems for finding DMR's, and I suspect they have low-quality data, and maybe that they are not following a correct pipeline.

Regards,
Gustavo

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