Hello, everyone :)

I'm trying to run the ChAMP SVD analysis, however I got an error which I don't fully understand. Anyone who does and knows how to solve?

First time I wrote down basic code

champ.svd()

[===========================]
[<<<<< ChAMP.SVD START >>>>>]
-----------------------------
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .

Error in if (class(beta) == "data.frame") { : 
  the condition has length > 1

And I got the error like above. However, I found that same as error as like me. Error using ChAMP SVD analysis It was really helpful to me.

But I faced a new error. Do you know how to modify this? I would appreciate it if it helped.

champ.SVD(beta=myNorm %>% as.data.frame(), pd=myLoad$pd)

[===========================]
[<<<<< ChAMP.SVD START >>>>>]
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .
Your beta parameter is data.frame format. ChAMP is now changing it to matrix.
[SVD analysis will be proceed with 780385 probes and 16 samples.]
[ champ.SVD() will only check the dimensions between data and pd, instead if checking if Sample_Names are correctly matched (because some user may
have no Sample_Names in their pd file),thus please make sure your pd file is in accord with your data sets (beta) and (rgSet).

<< Following Factors in your pd(sample_sheet.csv) will be analysised: >>

<Sample_Group>(character):control, case
<Sample_Well>(character):A01, B01, C01, D01, E01, F01, G01, H01
<Array>(character):R01C01, R02C01, R03C01, R04C01, R05C01, R06C01, R07C01, R08C01
<Slide>(character):200079600019, 200079600021
[champ.SVD have automatically select ALL factors contain at least two different values from your pd(sample_sheet.csv), if you don't want to analysis some of them, please remove them manually from your pd variable then retry champ.SVD().]

<< Following Factors in your pd(sample_sheet.csv) will not be analysis: >>
<Sample_Name>
<Sample_Plate>
<Pool_ID>
<Project>
<Basename>
<filenames>
[Factors are ignored because they only indicate Name or Project, or they contain ONLY ONE value across all Samples.]

<< PhenoTypes.lv generated successfully. >>
<< Calculate SVD matrix successfully. >>
Error in 1:ncol(svd.obj$v) : argument of length 0

I check my pd(*csv file) I think my Sentrix_ID keeps like "2.00923E+11". I changed into numeric but when I saved the pile in csv file, it keeps changes like that.

If you have any ways to help me, I would really be grateful if you can tell me comfortably.

Kind regards, seohyun