error while using champ.svd() function
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sinha.puja ▴ 10
@sinhapuja-18708
Last seen 4.1 years ago

Hi,

I am trying to analyze Illumina EPIC methylation array data with Champ.

and getting the following error when run champ.svd() :

<< PhenoTypes.lv generated successfully. >>
Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : 
  subscript out of bounds

Any ideas or help is appreciated.

 

THANKS!

champ • 2.2k views
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Can I have a look at your code? especially pheno parameter. I just tried to run it and seems working well.

I suspect your beta matrix and pheno are not matched with each other.

Best

Yuan Tian

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My code is:

if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")
BiocManager::install("ChAMP")
library(ChAMP)
baseDir2 <- "/C:/Users/sinha.puja/Desktop/idats"
myLoad <- champ.load(directory = getwd(),arraytype="EPIC")
champ.QC()
myNorm <- champ.norm(beta=myLoad$beta,rgSet=myLoad$rgSet,mset=myLoad$mset,resultsDir="./CHAMP_Normalization/",method="BMIQ",plotBMIQ=TRUE,arraytype="EPIC",cores=3)
champ.SVD(beta = myNorm,rgSet=myLoad$rgSet,pd=myLoad$pd,RGEffect=TRUE,PDFplot=TRUE,Rplot=TRUE,resultsDir="./CHAMP_SVDimages/")

but after running this I got an error:

champ.SVD Results will be saved in ./CHAMP_SVDimages/ .

[SVD analysis will be proceed with 760639 probes and 30 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_Well>(character):A1, B1, C1, D1, E1, F1, G1, H1, A2, B2, C2, D2, E2, F2, G2, H2, A3, B3, C3, D3, E3, F3, G3, H3, A4, B4, C4, D4, E4, F4
<Sample_Group>(character):P, C
<Slide>(numeric):203021070021, 203021070022, 203021070073, 203021070013
<Array>(character):R01C01, R02C01, R03C01, R04C01, R05C01, R06C01, R07C01, R08C01
<Category>(character):Pain, Control
<Age>(integer):63, 61, 77, 81, 74, 56, 60, 83, 69, 70, 75, 66, 65, 67, 80, 79, 68, 78, 71
<Female_Recode_1>(integer):1, 0
[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>
[Factors are ignored because they only indicate Name or Project, or they contain ONLY ONE value across all Samples.]
If you want to check Effect of Control Probes, you MUST provide rgSet parameter. Now champ.SVD can only analysis factors in pd.

<< PhenoTypes.lv generated successfully. >>
Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : 
  subscript out of bounds

Any help to troubleshoot this error will be greatly appreciated.

Thanks.

 
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Hi Puja: Please try use as.character function to reset your Slide column in pd. then retry It.The error could be triggered When your Slide column is numeric type. Best Yuan Tian
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Hi Yuan, I tried using as.character function but again it gives me the same type of error as mentioned in the upper section.

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Um... Please try convert both Slide and Female_Recode into factor or character, then retry it. I believe they should be category right? But according to the above output, they will all be considered as a numeric variable.

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