Why are there several gene expression files (for example, miRNA) in TCGA for one case?
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3 months ago

Hello I am working on gene expression data at TCGA Now I realized that for a case and a miRNA-Seq, for example, mirna-isoform, there is more than one gene expression file and the counts are different!

enter image description here

update: the cases are --> https://pastecode.io/s/j79ti1me

Do I have to merge these files together for analysis?

Differential expression TCGA miRNA gene • 551 views
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3 months ago
Zhenyu Zhang ★ 1.1k

Sequencing was done in aliquot level, so does the GDC analysis. If the case has more than one miRNA-Seq aliquots, you will have multiple miRNA-Seq analysis.

If you are doing multi-omics analysis, pick one that is on the same or similar aliquots of your other analysis. Otherwise, if you can confirm that they are from the same sample, merge is not wrong, but you will waste your energy explaining this to editors in the future.

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Thank you very much

Based on TCGA barcodes:

enter image description here

Are the following two samples similar for compare?

TCGA-AA-3531-01A-01T-0822-13

TCGA-AA-3531-01A-21H-1838-13

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They are from the same sample, but different aliquots. If you don't have other omics data to compare with, I will pick the one with later plate number.

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