Error with champ.CNA processing

[thscandolara]

Hi Yuan!

I'm encountering some problems with the following command champ.CNA. As recommended, I ran the batch effect correction for intensity values before champ.CNA analysis:

myintensity <- champ.runCombat(beta = myLoad$intensity, logitTrans = F, pd = myLoad$pd, variablename = "Sample_type")

After this, I tried to get CNA data but faced an error:

`> myCNA <- champ.CNA(intensity = myintensity,
+                    pheno = myLoad$pd$Sample_type,
+                    controlGroup = "NORMAL",
+                    arraytype = "EPIC")
[===========================]
[<<<<< ChAMP.CNA START >>>>>]
-----------------------------
champ.CNA Results will be saved in ./CHAMP_CNA .

ChaMP.CNA does not provide batch Correct on intensity data now, but you can use champ.runCombat to correct slides batch yourself.
<< Create Control Data >>
<< Calculate mean value difference between each sample to mean control samples >>
<< Generate CHR and MAPINFO information >>
<< Processing Samples >>
Analyzing: X.qn 
Error in sampleResult[[colnames(intsqnlogratio)[i]]] <- seg : 
  attempt to select less than one element in OneIndex
In addition: Warning message:
In champ.CNA(intensity = myintensity, pheno = myLoad$pd$Sample_type,  :
  NaNs produced`

I checked the source code but I really have no idea why I am getting this error (I have attached a print of my R screen).
What am I doing wrong?

Many thanks in advance!