Question: GDC legacy archive: get sample sheet containing sample_group and sample_ source for methylation data
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gravatar for daniellemo
8 months ago by
daniellemo0
Queen's University
daniellemo0 wrote:

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?

ADD COMMENTlink modified 8 months ago by Kevin Blighe45k • written 8 months ago by daniellemo0
1
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

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

ADD COMMENTlink modified 8 months ago • written 8 months ago by Kevin Blighe45k
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