Hi. This is a hard-to-troubleshoot problem. This could be due to one or more arrays having weak/noisy signals, or possibly even being corrupt.
As a first small step, I've created feature request https://github.com/HenrikBengtsson/calmate/issues/7. When that is in place, one can narrow down the problematic data and make the estimator more robust. /Henrik On Thu, Sep 13, 2018 at 7:37 AM <thomas.grombac...@merckgroup.com> wrote: > > I forgot the traceback: > > traceback() > 11: stop("singular matrix 'a' in solve") > 10: qr.solve(t(TR) * wgths^2, t(Genotypes) * wgths^2) > 9: fitCalMaTeMedians(dataInit, references = references, fB1 = fB1, > fB2 = fB2) > 8: fitFcn(Cjj, references = references, ...) > 7: calmateByThetaAB.array(theta, references = references, ..., verbose = > verbose) > 6: calmateByThetaAB(theta, references = references, ..., verbose = verbose) > > > Am Donnerstag, 13. September 2018 16:35:14 UTC+2 schrieb > thomas.g...@merckgroup.com: >> >> Hello, >> >> I am using CALMATE 0.12.1 to improve ASCN for a 1213 sample SNP6 data set >> without reference samples. >> I run the analysis on a 32core 156Gb main memory server. When CALMATE is >> fitting the model the following error occurs: >> >> ... >> setOption(aromaSettings, "memory/ram", 10.0) >> ... >> cmt <- CalMaTeCalibration(dsNList) >> dsCList <- process(cmt, verbose=verbose) >> ... >> 20180913 09:41:43| Fitting CalMaTe... >> 20180913 09:41:43| Algorithm flavor: v2 >> 20180913 09:41:43| Number of SNPs: 515251 >> 20180913 09:41:43| Number of SNPs left: 515251, 514751, 514251, 513751, >> 513251, 512751, 512251, 511751, 511251, 510751, 510251, 509751, 509251, >> 508751, 508251, 507751, 507251, 506751, 506251, 505751, 505251, 504751, >> 504251, 503751, 503251, 502751, 502251, 501751, 501251, 500751, 500251, >> 499751, 49925 >> ... >> 288251, 287751, 287251, 286751, 286251, 285751, 285251, 284751, 284251, >> 283751, 283251, 282751, 282251, 281751, 281251, 280751, 280251, 279751, >> 279251, 278751, 278251, 277751, 277251, Error in qr.solve(t(TR) * wgths^2, >> t(Genotypes) * wgths^2) : >> singular matrix 'a' in solve >> >> >> I tried a second run which leads to a similar error: >> ... >> 20180913 15:49:54| All data points are finite. >> 20180913 15:49:54| Identifying non-finite data points...done >> 20180913 15:49:54| Fitting CalMaTe... >> 20180913 15:49:54| Algorithm flavor: v2 >> 20180913 15:49:54| Number of SNPs: 51525 >> 20180913 15:49:54| Number of SNPs left: 51525, 51025, 50525, 50025, >> 49525, 49025, 48525, 48025, 47525, 47025, 46525, 46025, 45525, 45025, 44525, >> 44025, 43525, 43025, 42525, 42025, 41525, 41025, 40525, 40025, 39525, 39025, >> 38525, 38025, 37525, 37025, 36525, 36025, 35525, 35025, 34525, 34025, 33525, >> 33025, 32525, 32025, 31525, 31025, 30525, 30025, 29525, 29025, 28525, 28025, >> 27525, 27025, 26525, 26025, 25525, 25025, 24525, 24025, 23525, 23025, 22525, >> 22025, 21525, 21025, 20525, 20025, 19525, Error in qr.solve(t(TR) * wgths^2, >> t(Genotypes) * wgths^2) : >> singular matrix 'a' in solve >> >> >> >> >> And I get then the downstream error when I try to access the fitted >> fractionB data: >> >> dsCTxt<- writeDataFrame(dsCList$fracB, columns=c("unitName", "chromosome", >> "position", "*")) >> Error in writeDataFrame(dsCList$fracB, columns = c("unitName", "chromosome", >> : object 'dsCList' not found >> >> >> Any suggestion how to find the cause of error and a resolution ? >> >> >> > sessionInfo() >> R version 3.5.1 (2018-07-02) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> Running under: Windows 7 x64 (build 7601) Service Pack 1 >> >> Matrix products: default >> >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >> LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >> [5] LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] calmate_0.12.1 aroma.light_3.10.0 aroma.affymetrix_3.1.1 >> aroma.core_3.1.3 R.devices_2.16.0 >> [6] R.filesets_2.12.1 R.utils_2.7.0 R.oo_1.22.0 >> affxparser_1.52.0 R.methodsS3_1.7.1 >> >> loaded via a namespace (and not attached): >> [1] matrixStats_0.54.0 codetools_0.2-15 listenv_0.7.0 future_1.9.0 >> digest_0.6.16 MASS_7.3-50 R.huge_0.9.0 >> [8] future.apply_1.0.1 PSCBS_0.64.0 tools_3.5.1 R.cache_0.13.0 >> parallel_3.5.1 compiler_3.5.1 base64enc_0.1-3 >> [15] aroma.apd_0.6.0 R.rsp_0.43.0 globals_0.12.2 DNAcopy_1.54.0 >> >> >> best regards >> Thomas >> > -- > -- > 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/d/optout. -- -- 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/d/optout.
