[BioC] Newbie methylation and stats question

[Gustavo Fernández Bayón]

Hi Yao.

First of all, thank you for your answer.  

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Enviado con Sparrow (http://www.sparrowmailapp.com/?sig)


El martes 19 de junio de 2012 a las 16:46, Yao Chen escribió:

> As for as I know, this is no standard normalization for methylation data.  

As I have said to Tim in a previous post, I really thought I did not have to deal with normalization issues. Now it seems I have to start worrying about it.  
> For me, I prefer keeping the raw value and just adjusting the technical variants. Anyone has better solution. Please let me know.

I thought that, for a beginner like me, it was better not to deal with the normalization stages, and just start working with the beta values.  
>  
> Back the question, I agree with Mark. It's unusual to compare different region. These regions may have different background methylation status and hardly to directly compare.

Thanks to you three, I think I start to see things clear. The fact is that I just didn't know how to put it down in words. We should not compare the methylation status of different regions because their magnitudes and behaviors are not comparable. Am I getting near it?  
>  
> Jack
Regards,
Gustavo