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YuanTian1991 / ChAMP

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champ.QC() cmdscale() #10

Closed alliekarz closed 4 years ago

alliekarz commented 4 years ago

Hello,

I'm using champ in RStudio Version 1.2.1335, starting with a beta matrix as the IDAT files were not available.

I'm able to use champ.filter with no problem, but champ.QC() gives me the following error:

[===========================]
[<<<<< ChAMP.QC START >>>>>>]
-----------------------------
champ.QC Results will be saved in ./CHAMP_QCimages/
[QC plots will be proceed with 412481 probes and 40 samples.]
<< Prepare Data Over. >>
**Error in cmdscale(d) : NA values not allowed in 'd'**

My code is as follows:


library(ChAMP)
library(ChAMPdata)

myLoad <- champ.filter(beta=betas_matrix_n, pd=pd)
CpG.GUI(CpG = rownames(betas_matrix_n), arraytype = "450K")

champ.QC(beta=myLoad$beta, pheno=myLoad$pd$Sample_Group)

Thank you!!