Hi all, I wanted to change the default parameters of the glad algorithm. This does not work:
glad <- GladModel(cesN, lambdabreak=20, param=c(d=20)) fit(glad, arrays=1, chromosomes=22, verbose=verbose) [...] 20140214 21:18:11| Setting up GLAD data structure...done 20140214 21:18:11| User and segmentation arguments: List of 2 $ lambdabreak: num 20 $ param : Named num 20 ..- attr(*, "names")= chr "d" 20140214 21:18:11| Final arguments: List of 2 $ :List of 1 ..$ profileValues:'data.frame': 43799 obs. of 5 variables: .. ..$ LogRatio : num [1:43799] 0.07282 -0.03324 0.07527 0.00626 0.09242 ... .. ..$ PosOrder : int [1:43799] 1 2 3 4 5 6 7 8 9 10 ... .. ..$ Chromosome : int [1:43799] 22 22 22 22 22 22 22 22 22 22 ... .. ..$ PosBase : num [1:43799] 16052543 16052647 16060231 16061342 16066888 ... .. ..$ ChromosomeChar: int [1:43799] 22 22 22 22 22 22 22 22 22 22 ... ..- attr(*, "class")= chr "profileCGH" $ verbose: logi TRUE 20140214 21:18:11| Setting up method arguments...done 20140214 21:18:11| Looking for cached results... 20140214 21:18:11| Looking for cached results...done 20140214 21:18:11| Calling glad() of GLAD... [...] Although the paramaters appear in the log as optional arguments and I removed the gladModel directory on my disk, I always get the same results as with the default arguements. Running glad() manually works: cn <- extractRawCopyNumbers(glad, array=1, chromosome=22) data <- as.data.frame(cn) colnames(data) <- c("Chromosome", "Position", "LogRatio") data$PosOrder <- order(data$Position) library("GLAD") profile <- as.profileCGH(data) res <- glad(profile, lambdabreak=20, param=c(d=20)) Over segmentation is much reduced. I wonder whether it is correct to pass the arguments to the GladModel constructor. It seems to work according to what I read in this forum. Thanks and best regards, Hans-Ulrich > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GLAD_2.26.0 aroma.light_1.32.0 matrixStats_0.8.12 [4] aroma.affymetrix_2.11.1 aroma.core_2.11.0 R.devices_2.7.2 [7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8 [10] affxparser_1.34.0 R.methodsS3_1.5.2 loaded via a namespace (and not attached): [1] aroma.apd_0.4.0 digest_0.6.4 DNAcopy_1.36.0 PSCBS_0.40.2 [5] R.cache_0.9.0 R.huge_0.6.0 R.rsp_0.9.28 tools_3.0.1 -- -- 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.