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

ADD REPLY

Login before adding your answer.

Traffic: 432 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6