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Question: Normalization necessary for TCGA 450K data?
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gravatar for mbk0asis
4.5 years ago by
mbk0asis • 610
Korea, Republic Of
mbk0asis • 610 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 • 1.5k views
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modified 4.5 years ago by igor ♦ 12k • written 4.5 years ago by mbk0asis • 610
0
gravatar for igor
4.5 years ago by
igor ♦ 12k
United States
igor ♦ 12k 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 COMMENT • link modified 4.5 years ago • written 4.5 years ago by igor ♦ 12k
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 REPLY • link modified 4.5 years ago • written 4.5 years ago by mbk0asis • 610
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