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
1 answer
Current as of 4th September 2018:
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The link is no longer accessible to many. I saved the information on GitHub:
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?
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