Dear Henrik, I am trying to run my set of samples with the new code you sent me using version 0.35.0 of PSCBS. I get the following error when I try to run estimateKappa()
> kappa <- estimateKappa(fit, verbose=-10); Estimate global background (including normal contamination and more)... Number of segments: 152 Estimating threshold Delta0.5 from the empirical density of C1:s... adjust: 1 minDensity: 0.2 Error: nrow(fit) >= 2 is not TRUE Estimating threshold Delta0.5 from the empirical density of C1:s...done Estimate global background (including normal contamination and more)...done > str(fit) List of 5 $ data : Classes ‘PairedPSCNData’ and 'data.frame': 1873116 obs. of 8 variables: ..$ chromosome: int [1:1873116] 1 1 1 1 1 1 1 1 1 1 ... ..$ x : num [1:1873116] 61736 61809 61824 62153 62921 ... ..$ CT : num [1:1873116] 1.43 1.52 1.56 2.75 2.16 ... ..$ betaT : num [1:1873116] NA NA NA NA NA NA NA NA NA NA ... ..$ betaTN : num [1:1873116] NA NA NA NA NA NA NA NA NA NA ... ..$ muN : num [1:1873116] NA NA NA NA NA NA NA NA NA NA ... ..$ betaN : num [1:1873116] NA NA NA NA NA NA NA NA NA NA ... ..$ rho : num [1:1873116] NA NA NA NA NA NA NA NA NA NA ... $ output :Classes ‘PairedPSCNSegments’ and 'data.frame': 285 obs. of 16 variables: ..$ chromosome : int [1:285] 1 1 1 1 1 1 1 1 1 1 ... ..$ tcnId : int [1:285] 1 2 3 4 5 6 7 8 9 10 ... ..$ dhId : int [1:285] 1 1 1 1 1 1 1 1 1 1 ... ..$ tcnStart : num [1:285] 6.17e+04 1.29e+07 1.34e+07 5.62e+07 1.09e+08 ... ..$ tcnEnd : num [1:285] 1.29e+07 1.34e+07 5.62e+07 1.09e+08 1.13e+08 ... ..$ tcnNbrOfLoci: int [1:285] 6752 70 25226 35543 2840 21 5325 0 3044 34 ... ..$ tcnMean : num [1:285] 2.05 2.63 2.05 1.99 2.04 ... ..$ tcnNbrOfSNPs: int [1:285] 3432 15 12233 17668 1504 1 2625 0 1173 0 ... ..$ tcnNbrOfHets: int [1:285] 904 2 3168 4450 385 1 641 0 270 0 ... ..$ dhStart : num [1:285] 6.17e+04 1.29e+07 1.34e+07 5.62e+07 1.09e+08 ... ..$ dhEnd : num [1:285] 1.29e+07 1.34e+07 5.62e+07 1.09e+08 1.13e+08 ... ..$ dhNbrOfLoci : int [1:285] 904 2 3168 4450 385 1 641 NA 270 0 ... ..$ dhMean : num [1:285] 0.1119 0.0822 0.1012 0.0994 0.1073 ... ..$ c1Mean : num [1:285] 0.911 1.207 0.923 0.897 0.911 ... ..$ c2Mean : num [1:285] 1.14 1.42 1.13 1.09 1.13 ... ..$ rohCall : logi [1:285] FALSE FALSE FALSE FALSE FALSE FALSE ... $ tcnSegRows:'data.frame': 285 obs. of 2 variables: ..$ startRow: int [1:285] 1 6753 6823 32049 67592 70432 70453 NA 75778 78822 ... ..$ endRow : int [1:285] 6752 6822 32048 67591 70431 70452 75777 NA 78821 78855 ... $ dhSegRows :'data.frame': 285 obs. of 2 variables: ..$ startRow: int [1:285] 36 6753 6841 32079 67594 70432 70540 NA 75779 NA ... ..$ endRow : int [1:285] 6648 6801 32043 67584 70419 70432 75753 NA 78820 NA ... $ params :List of 9 ..$ alphaTCN : num 0.009 ..$ alphaDH : num 0.001 ..$ flavor : chr "tcn&dh" ..$ tbn : logi FALSE ..$ joinSegments : logi TRUE ..$ knownSegments :'data.frame': 64 obs. of 3 variables: ....$ chromosome: int [1:64] 1 1 1 2 2 2 2 2 3 3 ... ....$ start : num [1:64] -Inf 1.21e+08 1.43e+08 -Inf 9.03e+07 ... .. ..$ end : num [1:64] 1.21e+08 1.43e+08 Inf 9.03e+07 9.16e+07 ... ..$ seed : int 4874 ..$ meanEstimators:List of 2 .. ..$ tcn: chr "mean" .. ..$ dh : chr "median" ..$ deltaROH : num 0.0833 - attr(*, "class")= chr [1:3] "PairedPSCBS" "PSCBS" "AbstractCBS" If I skip this command, the same error comes at subsequent steps. I have sent you an email with a link to the object in case you need it. Thanks in advance, Oscar Oscar M. Rueda, PhD. Postdoctoral Research Fellow, Caldas Lab, Breast Cancer Functional Genomics. University of Cambridge. Cancer Research UK Cambridge Institute. Li Ka Shing Centre, Robinson Way. Cambridge CB2 0RE England -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
