Difficulty creating summarized experiment

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jasmine_chappell • 0

@21282318

Last seen 15 months ago

United Kingdom

Hi,

I am trying to create a summarised experiment as shown in this youtube video https://www.youtube.com/watch?v=b7hmDfU0LTo but I am having trouble figuring out how to do that. Is there a function that allows you to create a summarized experiment object from Methylation array data?

sesame sesameData • 735 views

ADD COMMENT • link updated 17 months ago by zhouwanding ▴ 10 • written 17 months ago by jasmine_chappell • 0

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Have you tried just using SummarizedExperiment from beta value matrix with proper colData? see https://bioconductor.org/help/course-materials/2019/BSS2019/04_Practical_CoreApproachesInBioconductor.html

ADD REPLY • link 17 months ago zhouwanding ▴ 10

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I have not tried that yet, I have the beta values, I am just not sure how to put them in a matrix.

ADD REPLY • link 17 months ago jasmine_chappell • 0

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Like SummarizedExperiment(assay=betas) ? You need colData to describe the sample covariables. See the link above for more detail.

ADD REPLY • link 17 months ago zhouwanding ▴ 10

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