Batch ID in TCGA database

Question

[Na Sed]

Hi,

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

[Na Sed]

The answer is in comment.

Answer 1

[russhh]

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

[Na Sed]

Thank you.

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

[Kevin Blighe]

Current as of 4th September 2018:

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

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

• C: TCGA barcode documentation? TCGA wiki?
• https://github.com/kevinblighe/TCGAbarcode/blob/master/README.md
• https://github.com/kevinblighe/TCGAbarcode/blob/master/TCGAbarcode.pdf

[modarzi]

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?

[z]

Really helpful!!!!!!