[BioC] Error in sort(abs(diff(genomdat)))[1:n.keep]

[SeshanV at mskcc.org]

The error may be the result of your call rather than either of the packages. Note that your call has "sdundo=c(0,0), alpha=c(0.5,0.1)" whereas the defaults from the manual is "sdundo=c(1,2), alpha=c(0.05,0.01)." 

Venkat


-----Original Message-----
From: wwwrun at mamba.fhcrc.org [mailto:wwwrun at mamba.fhcrc.org] 
Sent: Friday, May 24, 2013 10:05 AM
To: bioconductor at r-project.org; gongkn at big.ac.cn
Cc: Seshan, Venkatraman E./Epidemiology-Biostatistics
Subject: Error in sort(abs(diff(genomdat)))[1:n.keep]


Hi all, I'm using a package ExomeCNV to call LOH and got an error in step "Combine multiple positions into LOH segments"
the.loh = multi.LOH.analyze(normal, tumor, all.loh.ls=list(eLOH), test.alpha=0.001, method="variance.f", sdundo=c(0,0), alpha=c(0.5,0.1))

Analyzing: Sample.1
Error in sort(abs(diff(genomdat)))[1:n.keep] : 
  only 0's may be mixed with negative subscripts In addition: Warning message:
In CNA(data$baf, strip.chr.name(data$chr), data$position, data.type = "binary") :
  markers with missing chrom and/or maploc removed

ExomeCNV actually implement package DNAcopy in this step, and I can't tell how to bypass this problem since the "n.keep" isn't from ExomeCNV's code. I would really appreciate your expertise, thank you.


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ExomeCNV_1.4         DNAcopy_1.34.0       BiocInstaller_1.10.1

loaded via a namespace (and not attached):
[1] tools_3.0.1


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