Hi All, I am analyzing my EPIC array methylation data using ChAMP package. Can I run ChAMP for 4 samples? While trying with 4 samples(2 cases and 2 controls), the following error occurred in SVD and Combat functions. Can someone help me rectify this error?
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .
[ 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).]
[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.]
<< PhenoTypes.lv generated successfully. >> Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : subscript out of bounds In addition: Warning messages: 1: In dir.create(resultsDir) : '.\CHAMP_SVDimages' already exists 2: In if (class(beta) == "data.frame") { : the condition has length > 1 and only the first element will be used
<< Start Correcting Slide >> ~Sample_Group
<environment: 0x000001fa25761fe0> Generate mod success. Started to run ComBat, which is quite slow... Found 1 genes with uniform expression within a single batch (all zeros); these will not be adjusted for batch. Found2batches Adjusting for1covariate(s) or covariate level(s) Error in ComBat(dat = beta, batch = batch, mod = mod, par.prior = TRUE) : The covariate is confounded with batch! Remove the covariate and rerun ComBat
Could you provide the structure of your pd file ?
str(myLoad$pd)
or corresponding code