Question: (Closed) Batch ID in TCGA database
2
gravatar for Na Sed
4.4 years ago by
Na Sed280
United States
Na Sed280 wrote:

Hi,

I have downloaded some data from TCGA and I need to remove their batch effects using 'combat' algorithm from sva package, but 'cmobat' function needs batch ID.

I do not know how can I find batch IDs for samples. In barcode of samples, there is not any batch ID?!

Does anyone know how can I find batch IDs in TCGA database?

Thanks

N

batch effect tcga R • 4.2k views
ADD COMMENTlink written 4.4 years ago by Na Sed280

The answer is in comment.

 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Na Sed280
3
gravatar for russhh
4.4 years ago by
russhh4.6k
UK, U. Glasgow
russhh4.6k wrote:

There is a batch ID within the sample barcode, namely the 'plate' id described here

ADD COMMENTlink written 4.4 years ago by russhh4.6k

Thank you.

I did not know I can use 'plate' as batch ID!!

ADD REPLYlink written 4.4 years ago by Na Sed280

Really helpful!!!!!!

ADD REPLYlink written 3.3 years ago by z0

Current as of 4th September 2018:

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The link is no longer accessible to many. I saved the information on GitHub:

ADD REPLYlink modified 11 months ago • written 11 months ago by Kevin Blighe47k
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