how to get the sequencing platform information

[aiwa1986]

Hi,

Thanks for TCGAbiolinks package, it is very useful. One thing i wonder, how i can get the information on platform for tcga samples, some cancers were sequenced on different platforms (such as GAII and Hiseq). I tried to look for it in clinical data, biospecimen data, tried a set of different functions and still can't find it. Which function in TCGAbiolinks i should use to get this information?

Thanks in advance, Best wishes, Tatiana

[tiagochst]

Sorry for the late reply.

That information is available in the legacy database https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.access%22,%22value%22:%5B%22open%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%5B%22Gene%20expression%22%5D%7D%7D%5D%7D, but I wasn't able to find it in the newer version. Maybe you should contact the GDC support support at nci-gdc.datacommons.io

On Thu, Oct 6, 2022 at 9:23 AM aiwa1986 @.***> wrote:

Hi,

Thanks for TCGAbiolinks package, it is very useful. One thing i wonder, how i can get the information on platform for tcga samples, some cancers were sequenced on different platforms (such as GAII and Hiseq). I tried to look for it in clinical data, biospecimen data, tried a set of different functions and still can't find it. Which function in TCGAbiolinks i should use to get this information?

Thanks in advance, Best wishes, Tatiana

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[aiwa1986]

thanks for your reply!