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epigen / RnBeads

Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
https://rnbeads.org/
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EPIC data normalization #41

Open TatiMoe opened 1 year ago

TatiMoe commented 1 year ago

I´m trying to normalize my data from an EPIC array. The SWAN normalization works fine. When trying the "illumina" method I always get this warning: Incompatible dataset and normalization method: not supported for HumanMethylationEPIC. Changed the method to "none" --> I assume this method is not going to work. But I would also like to try the bmiq method. Here, it says that the normalization is performed, but that all my samples are beeing skipped and therefore not normalized. Why? It´s not really showing me an ERROR so how can i fix this..?

schmic05 commented 1 year ago

Hi @TatiMoe ,

What kind of Input data are you using for RnBeads? Did you start with raw IDAT files? BMIQ requires that these raw signal intensities are available, so this might be the issue. Otherwise, you can also send me the complete analysis.log and I will have a look.

TatiMoe commented 1 year ago

Hey @schmic05,

yes, I started with the raw IDATs...