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zwdzwd / sesame

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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Missing Control Probes #176

Open nanabgh1 opened 2 months ago

nanabgh1 commented 2 months ago

Hi, I’m having trouble using the DyeBiasCorr function and keep running into the following error: "Error in normControls(sdf, average = TRUE): No normalization control probes found!" I hope someone can help me with this. Thank you very much!

zwdzwd commented 2 months ago

Hi thanks for catching. I think it's a bug. I just fixed it in the latest upload (version 1.23.9). But I think you can use dyeBiasNL which is more recommended and used now. Let me know if you still see the issue after updating.

nanabgh1 commented 2 months ago

Thanks for the quick answer! I still see the issue but dyeBiasNL works fine, thank you

zwdzwd commented 2 months ago

Great. Have you reached 1.23.9? dyeBiasCorr seems to work fine on my end.

nanabgh1 commented 2 months ago

yes... sesame version 1.23.9, sesameData 1.22.0 and ExperimentHub 2.12.0

zwdzwd commented 2 months ago

Hmm, does the following work for you

sdf = sesameDataGet("EPICv2.8.SigDF")[[1]]
sdf1 = dyeBiasCorr(sdf)
nanabgh1 commented 2 months ago

yes it does, Is the problem that in my sdf, the controls are listed as attr(* "controls") = 'data.frame'? If so, can you tell me how to resolve this? Thank you

zwdzwd commented 2 months ago

Ah, which platform EPIC? are you using? I forgot to ask.

nanabgh1 commented 2 months ago

I want to analyze both, but currently I am working with HM450