Dear Henrik,
Thanks for your prompt reply. When I type sessionInfo(), the output is as
follows,
>sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
[5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.12.0 aroma.light_1.24.0 aroma.cn_1.5.0
[4] aroma.core_2.12.1 R.devices_2.8.2 R.filesets_2.4.0
[7] R.utils_1.29.8 R.oo_1.18.0 affxparser_1.28.1
[10] R.methodsS3_1.6.1
loaded via a namespace (and not attached):
[1] aroma.apd_0.5.0 base64enc_0.1-1 digest_0.6.4
DNAcopy_1.30.0
[5] matrixStats_0.8.14 PSCBS_0.40.4 R.cache_0.9.2 R.huge_0.8.0
[9] R.rsp_0.15.0 tools_2.15.1
Is there any problem with the version of Aroma files? I just updated them
recently but the workspace was built a while ago.
Regards,
Clara
On Sunday, April 27, 2014 5:35:47 PM UTC+8, Clara Tang wrote:
>
> Hi,
>
> I am trying to perform cross platform normalization for CytoScan and Omni
> using MSCN but the program stops after smoothing. I imported the Affymetrix
> raw intensity data and called the totalCn and Baf using CRMAv2 and CalMate.
> LogR ratio (log2 scale) and BAF were extracted using GenomeStudio for Omni
> and imported as 2^LRR*2 and BAF into .total.asb and .fracB.asb
> respectively. Plotting the CN indicated similar level of mean intensities
> for both platforms (CN~1) and thereby I proceeded to perform the mscn.
> Smoothing looks normal but after that, the program seemed to stop while
> backtransforming.
>
> May I know how I can overcome the error of * smooth.spline(sKK, lambda,
> ...)*?? What's wrong in my data?
>
> Thanks a lot!!!!!!
>
> --Clara
>
> *P.S. Log file is pasted as below,*
>
> =====================================================
> *dsNList <- process(mscn, verbose=log)*
> 20140427 17:06:46|Multi-source normalize all samples...
> 20140427 17:06:46| Number of unique samples in all sets: 8
> chr [1:8] "9C" "9C-2" "2C" "2C-2" "4C" ...
> 20140427 17:06:46| Processing each array...
> 20140427 17:06:46| Sample #1 ('9C') of 8...
> 20140427 17:06:46| Identifying source data files...
> 20140427 17:06:46| Getting list tuple of data files for one sample...
> 20140427 17:06:46| Sample name: 9C
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47| Getting list tuple of data files for one
> sample...done
> [[1]]
> AromaUnitTotalCnBinaryFile:
> Name: 9C
> Tags: total
> Full name: 9C,total
> Pathname:
> totalAndFracBData/Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,CMTN,v2/CytoScanHD_Array/9C,total.asb
> File size: 10.77 MB (11288937 bytes)
> RAM: 0.01 MB
> Number of data rows: 2822125
> File format: v1
> Dimensions: 2822125x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20140421 18:35:53
> HKT</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><srcDataSet>Cytoscan,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY</srcDataSet><srcChipType>CytoScanHD_Array,monocell</srcChipType><srcFullName>9C,chipEffects</srcFullName><srcChecksum>7d70e31c6aa60b7d8664373333ad5452</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
>
> [[2]]
> AromaUnitTotalCnBinaryFile:
> Name: 9C
> Tags:9C,ratio,total
> Full name: 9C,9C,ratio,total
> Pathname: totalAndFracBData/Omni/HumanOmni2.5/9C,9C,ratio,total.asb
> File size: 9.08 MB (9519600 bytes)
> RAM: 0.01 MB
> Number of data rows: 2379855
> File format: v1
> Dimensions: 2379855x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20140427 16:14:31
> HKT</createdOn><platform>Illumina</platform><chipType>HumanOmni2.5</chipType>
> Platform: Illumina
> Chip type: HumanOmni2.5
>
> 20140427 17:06:47| Identifying source data files...done
> 20140427 17:06:47| Check if all arrays are already normalized...
> 20140427 17:06:47| Is done: FALSE
> 20140427 17:06:47| Check if all arrays are already normalized...done
> 20140427 17:06:47| Fitting model...
> 20140427 17:06:47| Fitting one sample across multiple sources...
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47| Sample name: 9C
> List of 4
> $ subsetToFit : int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
> $ fitUgp :Classes 'AromaUgpFile',
> 'AromaUnitChromosomeTabularBinaryFile', 'AromaUnitTabularBinaryFile',
> 'UnitAnnotationDataFile', 'AromaMicroarrayTabularBinaryFile',
> 'AromaPlatformInterface', 'AromaTabularBinaryFile',
> 'FileCacheKeyInterface', 'CacheKeyInterface', 'GenericTabularFile',
> 'ColumnNamesInterface', 'GenericDataFile', 'FullNameInterface', 'Object'
> atomic [1:1] NA
> .. ..- attr(*, ".env")=<environment: 0x3c8f518>
> $ align : chr "byChromosome"
> $ targetDimension: int 1
> 20140427 17:06:47| Getting list tuple of data files for one sample...
> 20140427 17:06:47| Sample name: 9C
> 20140427 17:06:47| Number of arrays: 2
> 20140427 17:06:47| Getting list tuple of data files for one
> sample...done
> List of 2
> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
> 'FullNameInterface', 'Object' atomic [1:1] NA
> .. ..- attr(*, ".env")=<environment: 0x67be7f0>
> $ :Classes 'AromaUnitTotalCnBinaryFile', 'CopyNumberDataFile',
> 'AromaUnitSignalBinaryFile', 'AromaPlatformInterface',
> 'AromaTabularBinaryFile', 'FileCacheKeyInterface', 'CacheKeyInterface',
> 'GenericTabularFile', 'ColumnNamesInterface', 'GenericDataFile',
> 'FullNameInterface', 'Object' atomic [1:1] NA
> .. ..- attr(*, ".env")=<environment: 0x36d2f48>
> 20140427 17:06:47| Extracting data...
> 20140427 17:06:47| Subset of units used for fitting:
> int [1:28781] 1 2 3 4 5 6 7 8 9 10 ...
> num [1:28781, 1:2] 0.561 0.566 0.798 0.861 0.81 ...
> V1 V2
> Min. :-0.7285 Min. :-1.9090
> 1st Qu.: 0.9677 1st Qu.: 0.9403
> Median : 0.9842 Median : 0.9838
> Mean : 0.9805 Mean : 0.9898
> 3rd Qu.: 0.9995 3rd Qu.: 1.0340
> Max. : 1.3343 Max. : 1.9075
> NA's :1865 NA's :1934
> 20140427 17:06:48| Extracting data...done
> 20140427 17:06:48| Fitting across-source normalization function...
> 20140427 17:06:48| Estimator for principal curves:
> function (Y, ...)
> - attr(*, "smoother")=function (lambda, xj, ...)
> - attr(*, "df")= num 5
> 20140427 17:07:52| Fitting time:
> user system elapsed
> 63.884 0.008 64.062
> 20140427 17:07:52| Direction of fitted curve ('lambda') was flipped
> such that it increases with the signal.
> 20140427 17:07:52| Processing time: 64.1 seconds
> List of 7
> $ s : num [1:28781, 1:2] 0.652 0.652 0.665 NA 0.836 ...
> $ tag : num [1:28781] 15371 15372 7262 NA 15373 ...
> $ lambda : num [1:28781] 1.99 1.99 1.93 NA 1.38 ...
> $ dist : num 31.6
> $ converged : logi TRUE
> $ nbrOfIterations: int 6
> $ call : language principal.curve(x = X, smoother = ..1,
> trace = trace)
> - attr(*, "class")= chr [1:2] "PrincipalCurve" "principal.curve"
> - attr(*, "processingTime")=Class 'proc_time' Named num [1:5] 63.8
> 0.004 63.975 0 0
> .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self"
> "elapsed" "user.child" ...
> 20140427 17:07:52| Fitting across-source normalization function...done
> 20140427 17:07:52| Calculating shift for each chromosome...
> 20140427 17:07:52| align=byChromosome
> 20140427 17:07:52| Chromosomes: 1-25
> 20140427 17:07:52| Grouping units by chromosome...
> List of 24
> $ Chr01: int [1:2472] 1 2 3 4 5 6 7 8 9 10 ...
> $ Chr02: int [1:2434] 2473 2474 2475 2476 2477 2478 2479 2480 2481
> 2482 ...
> $ Chr03: int [1:1995] 4907 4908 4909 4910 4911 4912 4913 4914 4915
> 4916 ...
> $ Chr04: int [1:1917] 6902 6903 6904 6905 6906 6907 6908 6909 6910
> 6911 ...
> $ Chr05: int [1:1810] 8819 8820 8821 8822 8823 8824 8825 8826 8827
> 8828 ...
> $ Chr06: int [1:1709] 10629 10630 10631 10632 10633 10634 10635
> 10636 10637 10638 ...
> $ Chr07: int [1:1589] 12338 12339 12340 12341 12342 12343 12344
> 12345 12346 12347 ...
> $ Chr08: int [1:1463] 13927 13928 13929 13930 13931 13932 13933
> 13934 13935 13936 ...
> $ Chr09: int [1:1405] 15390 15391 15392 15393 15394 15395 15396
> 15397 15398 15399 ...
> $ Chr10: int [1:1355] 16795 16796 16797 16798 16799 16800 16801
> 16802 16803 16804 ...
> $ Chr11: int [1:1350] 18150 18151 18152 18153 18154 18155 18156
> 18157 18158 18159 ...
> $ Chr12: int [1:1335] 19500 19501 19502 19503 19504 19505 19506
> 19507 19508 19509 ...
> $ Chr13: int [1:1142] 20835 20836 20837 20838 20839 20840 20841
> 20842 20843 20844 ...
> $ Chr14: int [1:1064] 21977 21978 21979 21980 21981 21982 21983
> 21984 21985 21986 ...
> $ Chr15: int [1:1004] 23041 23042 23043 23044 23045 23046 23047
> 23048 23049 23050 ...
> $ Chr16: int [1:900] 24045 24046 24047 24048 24049 24050 24051
> 24052 24053 24054 ...
> $ Chr17: int [1:817] 24945 24946 24947 24948 24949 24950 24951
> 24952 24953 24954 ...
> $ Chr18: int [1:778] 25762 25763 25764 25765 25766 25767 25768
> 25769 25770 25771 ...
> $ Chr19: int [1:639] 26540 26541 26542 26543 26544 26545 26546
> 26547 26548 26549 ...
> $ Chr20: int [1:637] 27179 27180 27181 27182 27183 27184 27185
> 27186 27187 27188 ...
> $ Chr21: int [1:470] 27816 27817 27818 27819 27820 27821 27822
> 27823 27824 27825 ...
> $ Chr22: int [1:496] 28286 28287 28288 28289 28290 28291 28292
> 28293 28294 28295 ...
> $ Chr23: int [1:1550] 28782 28783 28784 28785 28786 28787 28788
> 28789 28790 28791 ...
> $ Chr24: int [1:578] 30332 30333 30334 30335 30336 30337 30338
> 30339 30340 30341 ...
> 20140427 17:07:52| Grouping units by chromosome...done
> 20140427 17:07:52| Allocating matrix for smooth data...
> 20140427 17:07:52| RAM: 494760 bytes
> 20140427 17:07:52| Allocating matrix for smooth data...done
> 20140427 17:07:52| Loading and backtransforming *smoothed* data...
> 20140427 17:07:52| Source #1 ('9C,total') of 2...
> 20140427 17:07:52| Loading smoothed data...
> num [1:30910] 0.561 0.566 0.798 0.861 0.81 ...
> 20140427 17:07:52| Loading smoothed data...done
> 20140427 17:07:52| Backtransforming smoothed data...
> *Error in smooth.spline(sKK, lambda, ...) : *
> missing or infinite values in inputs are not allowed
> 20140427 17:07:52| Backtransforming smoothed data...done
> 20140427 17:07:52| Source #1 ('9C,total') of 2...done
> 20140427 17:07:52| Loading and backtransforming *smoothed* data...done
> 20140427 17:07:52| Calculating shift for each chromosome...done
> 20140427 17:07:52| Fitting one sample across multiple sources...done
> 20140427 17:07:52| Fitting model...done
> 20140427 17:07:52| Sample #1 ('9C') of 8...done
> 20140427 17:07:52| Processing each array...done
> 20140427 17:07:52|Multi-source normalize all samples...done
>
>
--
--
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