TCGAbiolinks - fewer samples than expected

Question

[elmira.yazdii]

I utilized the TCGAbiolinks package for analyzing my data, through which I downloaded 571 samples. However, upon verifying the data in the TCGA database, I found only 507 samples. I confirmed that my data did not contain any duplicates. Additionally, when using GDCRNATools, I obtained 507 samples, consistent with the TCGA database. Could you please clarify the discrepancy in the sample numbers? This issue has left me perplexed.

[Ram]

Please ask https://support.bioconductor.org/

[Zhenyu Zhang]

What is this "TCGA database"? Do you mean GDC?

[elmira.yazdii]

yes, my means was GDC

[Zhenyu Zhang]

I suspect you mixed up three terms: case, sample, aliquot.