I have been running into an error while running champ.CNA() on a single array and I don't know how to solve it. After running champ.load() on the single array, I call champ.CNA(). The result is this:
> myCNA = champ.CNA()
You have chosen Control as the reference and this does not exist in your sample sheet (column Sample_Group). The analysis will run with ChAMP blood controls.
champ.CNA is using the samples you have defined as champCtl as the reference for calculating copy number aberrations.
As you are using the ChAMP controls Combat cannot adjust for batch effects. Batch effects may affect your dataset.
Saving Copy Number information for each Sample
Error in sort(abs(diff(genomdat)))[1:n.keep] :
only 0's may be mixed with negative subscripts
traceback() shows this:
3: trimmed.variance(genomdat[ina], trim)
Any help with this error would be much appreciated. Thanks in advance and let me know if you all have any questions which can better help you help me.