Question

error while using champ.svd() function

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sinha.puja ▴ 10

@sinhapuja-18708

Last seen 4.9 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 • 2.6k views

ADD COMMENT • link 6.1 years ago sinha.puja ▴ 10

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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

ADD REPLY • link 6.1 years ago Yuan Tian ▴ 290

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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.

ADD REPLY • link 6.1 years ago sinha.puja ▴ 10

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Entering edit mode

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

ADD REPLY • link 6.1 years ago Yuan Tian ▴ 290

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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.

ADD REPLY • link 6.0 years ago sinha.puja ▴ 10

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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.

ADD REPLY • link 6.0 years ago Yuan Tian ▴ 290