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GDC legacy archive: get sample sheet containing sample_group and sample_ source for methylation data

I am trying to follow the data cleaning workflow published in "A cross-package Bioconductor workflow for analyzing methylation array data", however some of the analyses require a sample sheet containing the sample source and sample group for each sample. I downloaded my methylation data from the GDC legacy archive, which does not allow you to download a sample sheet. Any way I can work around this and obtain the sample source and sample group data that I need?

methylation gdc legacy archive tcga sample sheet
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updated by Kevin Blighe Kevin Blighe • written by daniellemo • daniellemo

1 answer

You mean this tutorial: A cross-package Bioconductor workflow for analysing methylation array data

I would just create a custom sample sheet with minimal information. In it, you can also encode certain groups in relation to your samples. I believe it likely that much of the information, like Sample_Well, Slide, et cetera, will never be used.

Kevin

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written by Kevin Blighe Kevin Blighe

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