Error using ChAMP SVD analysis
1
0
Entering edit mode
FWNL15 • 0
@aba2f833
Last seen 12 months ago
Netherlands

I'm trying to run the ChAMP SVD analysis, however I get an error which I don't fully understand. Anyone who does and knows how to solve?

dir.create('./CHAMP_SVDimages')
champ.SVD(beta = mynormSPN,
rgSet=NULL,
pd=myloadSPN$pd, RGEffect=FALSE, PDFplot=TRUE, Rplot=TRUE, resultsDir="./CHAMP_SVDimages/SPN") [===========================] [<<<<< ChAMP.SVD START >>>>>] ----------------------------- champ.SVD Results will be saved in ./CHAMP_SVDimages/SPN . [SVD analysis will be proceed with 731946 probes and 15 samples.] [ champ.SVD() will only check the dimensions between data and pd, instead if checking if Sample_Names are correctly matched (because some user may have no Sample_Names in their pd file),thus please make sure your pd file is in accord with your data sets (beta) and (rgSet).] << Following Factors in your pd(sample_sheet.csv) will be analysised: >> <ï..Research.Number>(character):RD-17-592, RD-17-593, RD-17-594, RD-17-595, RD-17-596, RD-17-597, RD-17-598, RD-17-599, RD-17-600, RD-17-601, RD-17-602, RD-17-603, RD-17-604, RD-17-605, RD-17-606 <Stock.Conc..ng.uL>(numeric):11.3, 19, 11.8 <Slide>(numeric):202226320010, 202226320016 <Array>(character):R01C01, R02C01, R03C01, R04C01, R05C01, R06C01, R07C01, R08C01 [champ.SVD have automatically select ALL factors contain at least two different values from your pd(sample_sheet.csv), if you don't want to analysis some of them, please remove them manually from your pd variable then retry champ.SVD().] << Following Factors in your pd(sample_sheet.csv) will not be analysis: >> <Array.Type> <Sample_Name> [Factors are ignored because they only indicate Name or Project, or they contain ONLY ONE value across all Samples.] << PhenoTypes.lv generated successfully. >> Error in summary(lm(svd.o$v[, c] ~ PhenoTypes.lv[[f]]))$coeff[2, 4] : subscript out of bounds In addition: Warning message: In if (class(beta) == "data.frame") { : the condition has length > 1 and only the first element will be used  ChAMP • 556 views ADD COMMENT 0 Entering edit mode behr201 • 0 @336ed33e Last seen 6 months ago United Kingdom I think this error is caused by a column in your pd file having the wrong data type/class. In this case Slide probably needs to be a factor or character rather than numeric. The answer to this post explains it better than I can! ADD COMMENT 0 Entering edit mode In fact, I found that the author may have caused the problem  class(myNorm) %>% length() #equals 2 class(myNorm) == "data.frame" #So it will cause problems: the condition has length > 1 and only the first element will be used  u can code this champ.SVD(beta=myNorm %>% as.data.frame(), pd=myLoad$pd) to avoid it