Hi All, I have difficulty in running champ.SVD() . The following error is displayed. Can someone help me solve this? Thank you
champ.SVD Results will be saved in ./CHAMP_SVDimages/ .
[SVD analysis will be proceed with 716864 probes and 8 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>(integer):511435, 489411, 551531, 511436, 511437, 489415, 551517, 489417
<Sample_Group>(character):G1, G2, G3
<Slide>(numeric):204867380147, 204867380145
<Array>(character):R04C01, R01C01, R07C01, R05C01, R06C01, R02C01, R08C01, R03C01
<barcode>(character):204867380147_R04C01, 204867380145_R01C01, 204867380147_R07C01, 204867380147_R05C01, 204867380147_R06C01, 204867380145_R02C01, 204867380147_R08C01, 204867380145_R03C01
<Predicted.Male.Probability>(numeric):0.00244234513912241, 0.999992689783729, 0.999999635922064, 2.90635676791936e-06, 0.999958712708705, 1.35877147863061e-05, 0.999999550225184, 0.999997648444255
<Predicted.Gender>(character):female, male [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_Well>
<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
