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 -- Sent via the guest posting facility at bioconductor.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@mamba.fhcrc.org [mailto:wwwrun@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 -- Sent via the guest posting facility at bioconductor.org. ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.