error when using M-values in ChAMP
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a.mcneill • 0
@amcneill-14855
Last seen 6.2 years ago

when I load m-values for a differential methylation experiment in ChAMP I get the following error message with champ.norm, for both BMIQ and PBC. any suggestions welcome for how to solve?

 

Error in 1:ncol(beta) : argument of length 0
In addition: Warning messages:
1: In dir.create(resultsDir) : '.\CHAMP_Normalization' already exists
2: In min(beta, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf

 

ChAMP • 1.0k views
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Yuan Tian ▴ 270
@yuan-tian-13904
Last seen 2.5 years ago
United Kingdom

Hello:

I suspect you did not extract M value correctly because the error shows ncol(beta) is 0, which means you did not input a matrix. I suspect you used myLoad$beta (which is champ's default setting), but M matrix could be in myLoad$M.

Best

Yuan Tian

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a.mcneill • 0
@amcneill-14855
Last seen 6.2 years ago

thank you.

 

I also tried champ.load() with minfi, this permits normalisation to run - I will use the method you suggest

thanks

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