Hi All, I am following the code in the "Lab: CRMA v2 on 10K tumor data" document to process 147 SNP6.0 arrays. 39 of these arrays are from females and the rest are males. I am getting the following error message at the end of circular binary segmentation step:
Exception: Something is wrong with the data. Too many non-finite values: 36890 (25.2% > 20.0%) at throw(Exception(...)) at throw.default(sprintf("Something is wrong with the data. Too many non-finite values: %d (%.1f%% > at throw(sprintf("Something is wrong with the data. Too many non- finite values: %d (%.1f%% > %.1f%%)" at getRawCnData.CopyNumberChromosomalModel(this, ceList = ceList, refList = rfList, chromosome = chro at getRawCnData(this, ceList = ceList, refList = rfList, chromosome = chromosome, ..., estimateSd = F at extractRawCopyNumbers.CopyNumberChromosomalModel(this, array = array, chromosome = chr) at extractRawCopyNumbers(this, array = array, chromosome = chr) at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, verbose = verbose) at fit(this, ..., .retResults = FALSE, verbose = verbose) at plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png", plotband = plotband, arr at plot(model, p The sessionInfo is below: > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] 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] RColorBrewer_1.0-2 DNAcopy_1.22.1 sfit_0.1.9 aroma.affymetrix_1.7.0 aroma.apd_0.1.7 [6] affxparser_1.20.0 R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1 matrixStats_0.2.2 [11] R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.0 digest_0.4.2 R.utils_1.5.3 [16] R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] splines_2.11.1 I am assuming that this error is to the presence of two genders but of course I could be wrong. Can anyone provide an advice as to how to do this properly to avoid getting the same error? Should I run the "Vignette: Sex-chromosome bias-corrected reference signals from pooled average?" Thank you very much for your help... Mete -- 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/