Question: Batch ID in TCGA database
2
gravatar for Na Sed
5.2 years ago by
Na Sed290
United States
Na Sed290 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 • 4.8k views
ADD COMMENTlink written 5.2 years ago by Na Sed290

The answer is in comment.

 

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Na Sed290
3
gravatar for russhh
5.2 years ago by
russhh5.4k
UK, U. Glasgow
russhh5.4k wrote:

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

ADD COMMENTlink written 5.2 years ago by russhh5.4k
1

Thank you.

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

ADD REPLYlink written 5.2 years ago by Na Sed290
1

Current as of 4th September 2018:

--------------------------------------

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

ADD REPLYlink modified 21 months ago • written 21 months ago by Kevin Blighe60k

Dear Dr. Blighe I would like to have your comments about my 2 questions at TCGA batch effect process. I found that bach id in TCGA is a combine of "PlateId", "ShipDate", and ''Tissue Source Site". DX - Memorial Sloan Kettering is an example of a Tissue Source Site. am I right? and the second question is about batch effect removal time. Now I downloaded FPKM data from the GDC portal. can I remove batch effects on FPKM expression data? or I have to download HTSeq - Counts and then removing the batch effects and then normal it by FPKM method?

ADD REPLYlink written 6 months ago by modarzi120

Really helpful!!!!!!

ADD REPLYlink written 4.1 years ago by z0
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