How to identify the batch informations from the sample ID?
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12 months ago
DareDevil ★ 4.3k

I have thousands of samples from TCGA retrieved using TCGABiolinks. I want to remove the batch effect from the datasets. It's mentioned that batch can be detected from sample ID itself

How do we identify the batch info from the sample ID?

My ids look as follows.

TCGA-LL-A73Y-01A-11R-A33A-13
TCGA-AO-A03U-01B-21R-A10I-13
TCGA-E9-A1NH-01A-11R-A14C-13
TCGA-BH-A1EY-01A-11R-A13P-13
TCGA-AO-A1KS-01A-11R-A13P-13
TCGA-B6-A0I6-01A-11R-A035-13
TCGA-E9-A229-01A-31R-A156-13
TCGA-D8-A27H-01A-11R-A16E-13
TCGA-A2-A0EM-01A-11R-A035-13
TCGA-E2-A1II-01A-11R-A143-13
TCGA-BH-A0H3-01A-11R-A12O-13
TCGA-E2-A1IL-01A-11R-A14C-13
TCGA-BH-A0GY-01A-11R-A057-13
TCGA-BH-A0DG-01A-21R-A12O-13

I have looked at this link get information on sample ID, but not specifically mentioned about batches.

Is it a combination of PlateId, ShipDate, and Tissue Source Site or can I consider plates or tss as batch?

batch-correction TCGAbatch DESeq2 TCGA • 346 views
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