discrepancy in number of samples
0
0
Entering edit mode
@xiaofeiwang18266-13498
Last seen 15 months 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 • 1.2k views
ADD COMMENT
0
Entering edit mode

Kevin Blighe Do you have any ideas about this? Thank you so much!

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you so much!

ADD REPLY

Login before adding your answer.

Traffic: 636 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6