Missing Control Probes

[nanabgh1]

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]

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]

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

[zwdzwd]

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

[nanabgh1]

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

[zwdzwd]

Hmm, does the following work for you

sdf = sesameDataGet("EPICv2.8.SigDF")[[1]]
sdf1 = dyeBiasCorr(sdf)

[nanabgh1]

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]

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

[nanabgh1]

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