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
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