discrepancy in number of samples
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@xiaofeiwang18266-13498
Last seen 16 days ago
Singapore

Dear community,

I tried to download data by using "TCGAquery_recount2". But, I found the number of sample is different using different functions in TCGAbiolinks. Why does this happen? Thanks a lot!

If I used TCGAquery_recount2, the number of samples is 601 (542 Tumor and 58 Normal) for TCGA-LAUD. While it is 594 (535 T and 59 N) for TCGA-LUAD if I used "GDCquery", "GDCdownload", and "GDCprepare". The common samples are 594, and there are 7 more tumor samples using TCGAquery_recount2.

If I used TCGAquery_recount2 to download the GTEs data for Lung tissue, the number of samples is 374. But it is 419 from the GTEx website query. The common samples are 313 between these 2 ways.

TCGAquery_recount2 TCGAbiolinks • 107 views
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Kevin Blighe Do you have any ideas about this? Thank you so much!

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Hi, I think that TCGAbiolinks is downloading a different [older] version of the data. You could try to contact the TCGAbiolinks authors via the GitHub repository.

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Thank you so much!

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