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chrisamiller avatar chrisamiller commented on August 28, 2024

Hi @nesilin, I'm assuming that you solved the problem since you closed this, but feel free to reopen if that's not the case. Best of luck!

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nesilin avatar nesilin commented on August 28, 2024

Hi @chrisamiller !

I clearly had a data issue due to some error in the code so that 's why I closed the issue. But now that apparently everything is as expected I 'm getting two different errors depending on the sample:
For some samples I just get the same error as yesterday:

can't do clustering - no copy number 2 regions to operate on in sample 1 

which I don't understand because all the regions (genes) in the used sample have cn 2. As I mentioned yesterday, could I be having version issues like it seemed from here genome/sciclone-meta#1 ? I'm using the latest version of R and sciClone.

> sessionInfo()

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux release 6.7 (Carbon)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] devtools_1.12.0     sciClone_1.1.0      TeachingDemos_2.10 
 [4] MKmisc_0.991        plotrix_3.6-3       RColorBrewer_1.1-2 
 [7] rgl_0.95.1441       bmm_0.3.1           NORMT3_1.0-3       
[10] ggplot2_2.1.0       IRanges_2.6.1       S4Vectors_0.10.1   
[13] BiocGenerics_0.18.0 biomaRt_2.28.0      plyr_1.8.4         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5          AnnotationDbi_1.34.3 munsell_0.4.3       
 [4] colorspace_1.2-6     tools_3.3.0          Biobase_2.32.0      
 [7] gtable_0.2.0         DBI_0.4-1            withr_1.0.2         
[10] digest_0.6.9         bitops_1.0-6         RCurl_1.95-4.8      
[13] memoise_1.0.0        robustbase_0.92-6    RSQLite_1.0.0       
[16] DEoptimR_1.0-5       scales_0.4.0         XML_3.98-1.4        

For some other samples I get this other message:

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 5: negative widths are not allowed

which apparently isn't due to sciClone itself but to IRanges Have you seen this error before? Any idea of how to solve it?

Here is how I try to use sciClone:

sc <- sciClone(vafs=list(vafs[[1]]), copyNumberCalls=list(copyNumberCalls[[1]]), regionsToExclude=NULL,
               sampleNames=c('sample1'), minimumDepth=100, clusterMethod="bmm",
               clusterParams=NULL,
               cnCallsAreLog2=FALSE, useSexChrs=TRUE, doClustering=TRUE,
               verbose=TRUE, 
               copyNumberMargins=0.25, maximumClusters=10,
               annotation=NULL, doClusteringAlongMargins=TRUE,
               plotIntermediateResults=0)

Thank you in advance!

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chrisamiller avatar chrisamiller commented on August 28, 2024

Can you provide the head of your input files, along with the full script you're using to import the data and run sciclone (and the resulting log from running it)?

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