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:
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?
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:
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!