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zwdzwd / sesame

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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Imputation of missing beta values #109

Open andreyurch opened 1 year ago

andreyurch commented 1 year ago

Dear developers,

I found that in my dataset around 20% of probes are NA in 10% or less of the samples (different samples after general QC). Is there a way to impute the missing values with Seasame? Techniques like UMAP ask require only for complete cases.

Best regards, Andrey

zwdzwd commented 1 year ago

Hi Andrey,

There are many ways to impute data including taking the row means, using a fallback measurement, or a nearest neighbor-based method, and more. Alternatively, You can use openSesame(..., mask=FALSE) to turn off NA-masking. Hope that helps