Question: Normalization necessary for TCGA 450K data?
0
gravatar for mbk0asis
2.5 years ago by
mbk0asis410
Korea, Republic Of
mbk0asis410 wrote:

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!

normalization 450k • 985 views
ADD COMMENTlink modified 2.5 years ago by igor7.4k • written 2.5 years ago by mbk0asis410
0
gravatar for igor
2.5 years ago by
igor7.4k
United States
igor7.4k wrote:

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)?

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by igor7.4k
1

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by mbk0asis410
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