[aroma.affymetrix] CalMaTe model fitting error

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[aroma.affymetrix] CalMaTe model fitting error

thomas.grombacher
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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--
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[aroma.affymetrix] Re: CalMaTe model fitting error

thomas.grombacher
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 [hidden email]:
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/.
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Re: [aroma.affymetrix] Re: CalMaTe model fitting error

Henrik Bengtsson-2
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 <[hidden email]> 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 [hidden email]:
>>
>> 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 [hidden email]
> 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 [hidden email].
> 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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

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