I am trying to analyze Illumina EPIC methylation array data for a project. Since the project design was not done correctly, I am trying to subset/subdivide the samples into three groups, and do the differential comparisons within those groups. When I try to subset the data after the
myLoad object has been generated, I get an error asking me to check the dimensions of the subset, even though the dimensions of the matrices seem to be correct. When I change my SampleSheet file to just list those samples that I want to subset, and run
champ.svd(), I get the following error:
[===========================] [<<<<< ChAMP.SVD START >>>>>] ----------------------------- champ.SVD Results will be saved in ./CHAMP_SVDimages/ . [SVD analysis will be proceed with 741930 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_ID>(character):TCC1, TCC2, TCC3, TCC4, TCC5, TCP1, TCP2, TCP3, TCP4, TCP5, TCP6, TCP7, TCP8, TCP9, TCP10, TCP11 <Sample_Well>(character):A1, B1, C1, D1, E1, F1, G1, H1, A2, B2, C2, D2, E2, F2, G2, H2 <Sample_Group>(character):TCC, TCP <Slide>(numeric):201496710011, 201496710034 <Array>(character):R01C01, R02C01, R03C01, R04C01, R05C01, R06C01, R07C01, R08C01 <X>(factor):, . [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> [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
I am not sure what is going wrong, so any suggestions or help is appreciated. Thanks!