Normalization necessary for TCGA 450K data?

Question

[mbk0asis]

Hi, all.

I just downloaded 450K methylation data from TCGA and found that the data contain control probes for something.

I'm sure, but I'm guessing they are for normalization.

So, do I need to normalize the data using some tools, or can I just use it for analysis?

If I have to do the former one, which tool should I use?

Thank you!

Answer 1

[igor]

It depends on what format the data is in. You can download different files. Did you download the processed files (normalized) or the raw IDATs (not normalized)?

[mbk0asis]

I downloaded them from here. I'm not sure if they are normalized or not because there is no indication on that page.